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277 results on '"National Center for Biotechnology Information (NCBI)"'

1. Machine learning neuroprotective strategy reveals a unique set of Parkinson therapeutic nicotine analogs

Author: Intramural Research Program of the National Institutes of Health (USA), National Library of Medicine (USA), National Center for Biotechnology Information (NCBI), Rojas-Rodríguez, Felipe, Morantes, Carlos, Pinzón, Andrés, Barreto, George E., Cabezas, Ricardo, Mariño-Ramírez, Leonardo, González, Janneth, Intramural Research Program of the National Institutes of Health (USA), National Library of Medicine (USA), National Center for Biotechnology Information (NCBI), Rojas-Rodríguez, Felipe, Morantes, Carlos, Pinzón, Andrés, Barreto, George E., Cabezas, Ricardo, Mariño-Ramírez, Leonardo, and González, Janneth
Abstract: peer-reviewed, Aims: Present a novel machine learning computational strategy to predict the neuroprotection potential of nicotine analogs acting over the behavior of unpaired signaling pathways in Parkinson's disease. Background: Dopaminergic replacement has been used for Parkinson’s Disease (PD) treatment with positive effects on motor symptomatology but low progression and prevention effects. Epidemiological studies have shown that nicotine consumption decreases PD prevalence through neuroprotective mechanisms activation associated with the overstimulation of signaling pathways (SP) such as PI3K/AKT through nicotinic acetylcholine receptors (e.g α7 nAChRs) and over-expression of anti-apoptotic genes such as Bcl-2. Nicotine analogs with similar neuroprotective activity but decreased secondary effects remains as promissory field. Objective: Develop an interdisciplinary computational strategy predicting the neuroprotective activity of a series of 8 novel nicotine analogs over Parkinson's disease. Methods: We present a computational strategy integrating structural bioinformatics, SP manual reconstruction, and deep learning to predict the potential neuroprotective activity of 8 novel nicotine analogs over the behavior of PI3K/AKT. We performed a protein-ligand analysis between nicotine analogs and α7 nAChRs receptor using geometrical conformers, physicochemical characterization of the analogs and developed a manually curated neuroprotective datasets to analyze their potential activity. Additionally, we developed a predictive machine-learning model for neuroprotection in PD through the integration of Markov Chain Monte-Carlo transition matrix for the 2 SP with synthetic training datasets of the physicochemical properties and structural dataset. Results: Our model was able to predict the potential neuroprotective activity of seven new nicotine analogs based on the binomial Bcl-2 response regulated by the activation of PI3K/AKT. Conclusion: Hereby, we present a robust novel strategy to

2. Findings of the WMT 2020 Biomedical Translation Shared Task: Basque, Italian and Russian as New Additional Languages

Author: Bawden, Rachel, Di Nunzio, Giorgio, Grozea, Cristian, Unanue, Iñigo, Yepes, Antonio, Mah, Nancy, Martinez, David, Névéol, Aurélie, Neves, Mariana, Oronoz, Maite, Perez De Viñaspre, Olatz, Piccardi, Massimo, Roller, Roland, Siu, Amy, Thomas, Philippe, Vezzani, Federica, Navarro, Maika, Wiemann, Dina, Yeganova, Lana, School of Informatics [Edimbourg], University of Edinburgh, Universita degli Studi di Padova, Fraunhofer Institute FOKUS, Berlin, University of Technology Sydney (UTS), IBM Research Australia, Fraunhofer Institute for Biomedical Engineering (IBMT), Berlin, Laboratoire d'Informatique pour la Mécanique et les Sciences de l'Ingénieur (LIMSI), Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment [Berlin] (BfR), IXA NLP Group, University of the Basque Country/Euskal Herriko Unibertsitatea (UPV/EHU), Deutsches Forschungszentrum für Künstliche Intelligenz GmbH = German Research Center for Artificial Intelligence (DFKI), Beuth University of Applied Sciences, Department of Linguistic and Literary Studies, University of Padua, Maika Spanish Translator, Novartis Pharma AG, National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health [Bethesda] (NIH)-National Center for Biotechnology Information (NCBI), and National Institutes of Health [Bethesda] (NIH)
Subjects: Biomedical, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, Machine translation, Evaluation, Shared task, [INFO.INFO-CL]Computer Science [cs]/Computation and Language [cs.CL]
Abstract: International audience; Machine translation of scientific abstracts and terminologies has the potential to support health professionals and biomedical researchers in some of their activities. In the fifth edition of the WMT Biomedical Task, we addressed a total of eight language pairs. Five language pairs were previously addressed in past editions of the shared task, namely, English/German, English/French, English/Spanish, English/Portuguese, and English/Chinese. Three additional languages pairs were also introduced this year: English/Russian, English/Italian, and English/Basque. The task addressed the evaluation of both scientific abstracts (all language pairs) and terminologies (English/Basque only). We received submissions from a total of 20 teams. For recurring language pairs, we observed an improvement in the translations in terms of automatic scores and qualitative evaluations, compared to previous years.
Published: 2020

3. Origin of programmed cell death from antiviral defense?

Author: Koonin, Eugene V., Krupovic, Mart, National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health [Bethesda] (NIH)-National Center for Biotechnology Information (NCBI), Département de Microbiologie - Department of Microbiology, Institut Pasteur [Paris] (IP), and Institut Pasteur [Paris]
Subjects: Programmed cell death, [SDV]Life Sciences [q-bio], education, Cell, ENDOG, Biology, 03 medical and health sciences, Meiosis, Commentaries, Genetics, otorhinolaryngologic diseases, medicine, Fragmentation (cell biology), health care economics and organizations, 030304 developmental biology, 0303 health sciences, Multidisciplinary, urogenital system, 030306 microbiology, MESH: Antiviral Agents, MESH: Apoptosis, Biological Sciences, Cell biology, Nuclear DNA, Multicellular organism, medicine.anatomical_structure, DNA fragmentation
Abstract: Viruses and other genetic parasites are ubiquitous in the biosphere, and virtually all cellular organisms evolved multiple defense mechanisms to cope with onslaughts of these parasites (1). In multicellular life forms, a major class of such mechanisms is programmed cell death (PCD), whereby an infected cell “commits altruistic suicide” to prevent infection of other cells (2). Many unicellular eukaryotes and prokaryotes also possess PCD pathways but, in this case, the function and, especially, the evolution of such self-destructing mechanisms remain controversial topics because it is not immediately clear how unicellular organisms would benefit from suicide (3⇓–5). Models have been developed to account for the origin of PCD through population-level kin selection (5⇓–7) but the controversy persists. In a PNAS article, Gao et al. (8) present observations suggesting the possibility that some forms of PCD might have evolved from antivirus defense mechanisms. The experimental system is budding yeast sporulation that involves a meiotic division resulting in the development of spores and PCD of the remains of the mother cell (9, 10). This PCD is accompanied by fragmentation of the nuclear DNA of the dying cell that is catalyzed by the NUC1 nuclease released from the mitochondria. NUC1 belongs to the EndoG family of nucleases that is highly conserved among all eukaryotes and most prokaryotes and is responsible for DNA fragmentation during PCD in animals and at least some protists (11⇓–13). Thus, this phenomenon is widely conserved in evolution and yet remains somewhat enigmatic because DNA fragmentation is not required for PCD that occurs normally … [↵][1]1To whom correspondence may be addressed. Email: koonin{at}ncbi.nlm.nih.gov or krupovic{at}pasteur.fr. [1]: #xref-corresp-1-1
Published: 2019

4. Origin of viruses: primordial replicators recruiting capsids from hosts

Author: Mart Krupovic, Eugene V. Koonin, Valerian V. Dolja, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), Department of Botany and Plant Pathology, Oregon State University (OSU), National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health [Bethesda] (NIH)-National Center for Biotechnology Information (NCBI), E.V.K. is supported through the intramural programme of the US National Institutes of Health. M.K. was supported by the Agence Nationale de la Recherche (France) project ENVIRA (no. ANR-17-CE15-0005-01)., Nature Reviews Microbiology thanks Raul Andino, Purificación López-García, Didier Raoult and Yong-Zhen Zhang for their contribution to the peer review of this work., ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), and Institut Pasteur [Paris]
Subjects: viruses, [SDV]Life Sciences [q-bio], Morphogenesis, MESH: Capsid/metabolism, Biology, Microbiology, Genome, MESH: Biological Evolution, 03 medical and health sciences, Capsid, Polyphyly, Replicon, Viral evolution, Gene, 0303 health sciences, Host Microbial Interactions, General Immunology and Microbiology, 030306 microbiology, MESH: Host Microbial Interactions, Viral proteins, Virus structures, Biological Evolution, Infectious Diseases, MESH: Viruses/growth & development, Evolutionary biology, Viruses, MESH: Viruses/genetics, Viral genome replication
Abstract: International audience; Viruses are ubiquitous parasites of cellular life and the most abundant biological entities on Earth. It is widely accepted that viruses are polyphyletic, but a consensus scenario for their ultimate origin is still lacking. Traditionally, three scenarios for the origin of viruses have been considered: descent from primordial, precellular genetic elements, reductive evolution from cellular ancestors and escape of genes from cellular hosts, achieving partial replicative autonomy and becoming parasitic genetic elements. These classical scenarios give different timelines for the origin(s) of viruses and do not explain the provenance of the two key functional modules that are responsible, respectively, for viral genome replication and virion morphogenesis. Here, we outline a 'chimeric' scenario under which different types of primordial, selfish replicons gave rise to viruses by recruiting host proteins for virion formation. We also propose that new groups of viruses have repeatedly emerged at all stages of the evolution of life, often through the displacement of ancestral structural and genome replication genes.
Published: 2019

5. Improved reference genome of Aedes aegypti informs arbovirus vector control

Author: Adam M. Phillippy, Richard Hall, Michael R. Murphy, Vinita Joardar, Daniel E. Neafsey, Bradley J. White, Margaret Herre, Gareth D. Weedall, Steven D. Buckingham, Louis Lambrechts, Hugh M. Robertson, Andrew K. Jones, David B. Sattelle, Han Cao, Karla Saavedra-Rodriguez, Yang Wu, Maria V. Sharakhova, Allison M Weakley, Atashi Sharma, Alexander S. Raikhel, Olga Dudchenko, Catherine A. Hill, Sourav Roy, Saki Chan, Sara N. Mitchell, Alex Hastie, Arina D. Omer, Igor Filipović, Zhilei Zhao, Raissa G.G. Kay, Melissa Smith, Joyce Lee, Eric Cox, Sergey Koren, Li Zhao, Vidya Ramasamy, Benjamin J. Matthews, Joe Turner, William C. Black, Noah H. Rose, Leslie B. Vosshall, Erez Lieberman Aiden, Corey L. Campbell, Gordana Rašić, Zhijian Tu, J. Spencer Johnston, Jill Muehling, Jonas Korlach, Igor V. Sharakhov, Seth Redmond, Thanyalak Fansiri, Andrea Gloria-Soria, Omar S. Akbari, Aviva Presser Aiden, Richard S. Mann, Igor Antoshechkin, Jacob E. Crawford, Frederick A. Partridge, Alistair C. Darby, Sanjit S. Batra, Carolyn S. McBride, Sarah B. Kingan, Jeffrey R. Powell, Benjamin R. Evans, Gareth J Lycett, William J. Glassford, Paul Peluso, Shruti Sharan, Albin Fontaine, Carlos A Brito-Sierra, Terence Murphy, Vamsi K. Kodali, Rockefeller University [New York], Howard Hughes Medical Institute [New York] (HHMI), Howard Hughes Medical Institute (HHMI)-New York University School of Medicine, NYU System (NYU)-NYU System (NYU)-Rockefeller University [New York]-Columbia University Irving Medical Center (CUIMC), Kavli Neural Systems Institute, Baylor College of Medicine (BCM), Baylor University, Rice University [Houston], Pacific Biosciences [Menlo Park], Pacific Biosciences of California, National Human Genome Research Institute (NHGRI), California Institute of Technology (CALTECH), Verily Life Sciences Inc, Columbia University [New York], Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Harvard T.H. Chan School of Public Health, Princeton University, Liverpool John Moores University (LJMU), Virginia Tech [Blacksburg], Southern Medical University [Guangzhou], Purdue University [West Lafayette], University College of London [London] (UCL), Colorado State University [Fort Collins] (CSU), Bionano Genomics Inc, National Center for Biotechnology Information (NCBI), Yale University [New Haven], Armed Forces Research Institute of Medical Sciences [Bangkok] (AFRIMS), QIMR Berghofer Medical Research Institute, Interactions Virus-Insectes - Insect-Virus Interactions (IVI), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche Biomédicale des Armées [Antenne Marseille] (IRBA), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Oxford Brookes University, University of California [Riverside] (UC Riverside), University of California (UC), Liverpool School of Tropical Medicine (LSTM), University of Liverpool, University of California [San Diego] (UC San Diego), Texas A&M University [College Station], Tomsk State University [Tomsk], University of Illinois [Chicago] (UIC), University of Illinois System, Howard Hughes Medical Institute [New York], This research was supported in part by federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under grant number U19AI110818 to the Broad Institute (S.N.R. and D.E.N.), USDA 2017-05741 (E.L.A.), NSF PHY-1427654 Center for Theoretical Biological Physics (E.L.A.), NIH Intramural Research Program, National Library of Medicine and National Human Genome Research Institute (A.M.P. and S.K.) and the following extramural NIH grants: R01AI101112 (J.R.P.), R35GM118336 (R.S.M. and W.J.G.), R21AI121853 (M.V.S., I.V.S. and A.S.), R01AI123338 (Z.T.), T32GM007739 (M.H.), NIH/NCATS UL1TR000043 (Rockefeller University), DP2OD008540 (E.L.A.), U01AI088647, 1R01AI121211 (W.C.B. IV), Fogarty Training Grant D43TW001130-08, U01HL130010 (E.L.A.), UM1HG009375 (E.L.A), 5K22AI113060 (O.S.A.), 1R21AI123937 (O.S.A.), and R00DC012069 (C.S.M.), Defence Advanced Research Project Agency: HR0011-17-2- 0047 (O.S.A.). Other support was provided by Jane Coffin Childs Memorial Fund (B.J.M.), Center for Theoretical Biological Physics postdoctoral fellowship (O.D.), Robertson Foundation (L.Z.), and McNair & Welch (Q-1866) Foundations (E.L.A.), French Government’s Investissement d’Avenir program, Laboratoire d’Excellence Integrative Biology of Emerging Infectious Diseases (grant ANR-10-LABX-62-IBEID to L.L.), Agence Nationale de la Recherche grant ANR-17-ERC2-0016-01 (L.L.), European Union’s Horizon 2020 research and innovation program under ZikaPLAN grant agreement no. 734584 (L.L.), Pew and Searle Scholars Programs (C.S.M.), Klingenstein-Simons Fellowship in the Neurosciences (C.S.M.). A.M.W., B.J.W., J.E.C. and S.N.M. were supported by Verily Life Sciences. L.B.V. is an investigator of the Howard Hughes Medical Institute., We thank R. Andino, S. Emrich and D. Lawson (Vectorbase), A. A. James, M. Kunitomi, C. Nusbaum, D. Severson, N. Whiteman, T. Dickinson, M. Hartley and B. Rice (Dovetail Genomics) for early participation in the AGWG, C. Bargmann, D. Botstein, E. Jarvis and E. Lander for encouragement and facilitation. N. Keivanfar, D. Jaffe and D. M. Church (10X Genomics) prepared DNA for structural-variant analysis. We thank A. Harmon of the New York Times and acknowledge generous pro bono data and analysis from our corporate collaborators, ANR-17-ERC2-0016,GxG,Base génétique de la spécificité génotype-génotype dans l'interaction naturelle entre un virus et son insecte vecteur(2017), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), European Project: no. 734584, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), University of California [Riverside] (UCR), University of California, Biochemistry, Entomology, Fralin Life Sciences Institute, Howard Hughes Medical Institute (HHMI)-Rockefeller University [New York]-Columbia University Irving Medical Center (CUIMC)-New York University School of Medicine, NYU System (NYU)-NYU System (NYU), Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), The Rockefeller University [New-York], Howard Hughes Medical Institute [Berkeley], University of California [Berkeley], Baylor College of Medicine ( BCM ), Baylor College of Medicine, National Human Genome Research Institute ( NHGRI ), California Institute of Technology ( CALTECH ), Broad Institute of MIT and Harvard ( BROAD INSTITUTE ), Harvard Medical School [Boston] ( HMS ) -Massachusetts General Hospital [Boston] ( MGH ) -Massachusetts Institute of Technology ( MIT ), Liverpool John Moore University ( ljmu ), University College of London [London] ( UCL ), Colorado State University [Fort Collins] ( CSU ), National Center for Biotechnology Information ( NCBI ), Armed Forces Research Institute of Medical Sciences [Bangkok] ( AFRIMS ), Vecteurs - Infections tropicales et méditerranéennes ( VITROME ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Institut de Recherche Biomédicale des Armées ( IRBA ), Interactions Virus-Insectes - Insect-Virus Interactions ( IVI ), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Institut de Recherche Biomédicale des Armées [Antenne Marseille] ( IRBA ), University of California [Riverside] ( UCR ), Liverpool School of Tropical Medicine ( LSTM ), University of California [San Diego] ( UC San Diego ), and University of Illinois at Urbana-Champaign [Urbana]
Subjects: 0301 basic medicine, Male, and promotion of well-being, [SDV]Life Sciences [q-bio], Genome, Insect, Dengue virus, medicine.disease_cause, Dengue fever, Insecticide Resistance, Aedes, Pyrethrins, Chikungunya, Glutathione Transferase, Genetics, education.field_of_study, Multidisciplinary, Genome, biology, Yellow fever, Genomics, Reference Standards, 3. Good health, [ SDV.MHEP.MI ] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Infectious Diseases, Multigene Family, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Female, Infection, Biotechnology, DNA Copy Number Variations, General Science & Technology, 1.1 Normal biological development and functioning, Population, Aedes aegypti, Mosquito Vectors, Arbovirus Infections, Arbovirus, Insect Control, Article, Vaccine Related, 03 medical and health sciences, QH301, Rare Diseases, Underpinning research, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], medicine, Animals, education, QR355, 3.2 Interventions to alter physical and biological environmental risks, [SDV.GEN]Life Sciences [q-bio]/Genetics, Prevention, Human Genome, Genetic Variation, Molecular Sequence Annotation, Dengue Virus, Sex Determination Processes, medicine.disease, biology.organism_classification, Prevention of disease and conditions, Vector-Borne Diseases, 030104 developmental biology, Emerging Infectious Diseases, Good Health and Well Being, Genetics, Population, Vector (epidemiology), Insect, Arboviruses, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: Female Aedes aegypti mosquitoes infect more than 400 million people each year with dangerous viral pathogens including dengue, yellow fever, Zika and chikungunya. Progress in understanding the biology of mosquitoes and developing the tools to fight them has been slowed by the lack of a high-quality genome assembly. Here we combine diverse technologies to produce the markedly improved, fully re-annotated AaegL5 genome assembly, and demonstrate how it accelerates mosquito science. We anchored physical and cytogenetic maps, doubled the number of known chemosensory ionotropic receptors that guide mosquitoes to human hosts and egg-laying sites, provided further insight into the size and composition of the sex-determining M locus, and revealed copy-number variation among glutathione S-transferase genes that are important for insecticide resistance. Using high-resolution quantitative trait locus and population genomic analyses, we mapped new candidates for dengue vector competence and insecticide resistance. AaegL5 will catalyse new biological insights and intervention strategies to fight this deadly disease vector. National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services [U19AI110818]; USDA [2017-05741]; NIH Intramural Research Program; National Library of Medicine; National Human Genome Research Institute; NSF [PHY-1427654]; NIH [R01AI101112, R35GM118336, R21AI121853, R01AI123338, T32GM007739, NIH/NCATS UL1TR000043, DP2OD008540, U01AI088647, 1R01AI121211, D43TW001130-08, U01HL130010, UM1HG009375, 5K22AI113060, 1R21AI123937, R00DC012069]; Defence Advanced Research Project Agency [HR0011-17-2-0047]; Jane Coffin Childs Memorial Fund; Center for Theoretical Biological Physics postdoctoral fellowship; Robertson Foundation; McNair Foundation; Welch Foundation [Q-1866]; French Government's Investissement d'Avenir program, Laboratoire d'Excellence Integrative Biology of Emerging Infectious Diseases [ANR-10-LABX-62-IBEID]; Agence Nationale de la Recherche [ANR-17-ERC2-0016-01]; European Union [734584]; Pew and Searle Scholars Programs; Klingenstein-Simons Fellowship in the Neurosciences; Verily Life Sciences We thank R. Andino; S. Emrich and D. Lawson (Vectorbase); A. A. James, M. Kunitomi, C. Nusbaum, D. Severson, N. Whiteman; T. Dickinson, M. Hartley and B. Rice (Dovetail Genomics) for early participation in the AGWG; C. Bargmann, D. Botstein, E. Jarvis and E. Lander for encouragement and facilitation. N. Keivanfar, D. Jaffe and D. M. Church (10X Genomics) prepared DNA for structural-variant analysis. We thank A. Harmon of the New York Times and acknowledge generous pro bono data and analysis from our corporate collaborators. This research was supported in part by federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under grant number U19AI110818 to the Broad Institute (S.N.R. and D.E.N.); USDA 2017-05741 (E.L.A.); NSF PHY-1427654 Center for Theoretical Biological Physics (E.L.A.); NIH Intramural Research Program, National Library of Medicine and National Human Genome Research Institute (A.M.P. and S.K.) and the following extramural NIH grants: R01AI101112 (J.R.P.), R35GM118336 (R.S.M. and W.J.G.), R21AI121853 (M.V.S., I.V.S. and A. S.), R01AI123338 (Z.T.), T32GM007739 (M.H.), NIH/NCATS UL1TR000043 (Rockefeller University), DP2OD008540 (E.L.A.), U01AI088647, 1R01AI121211 (W.C.B. IV), Fogarty Training Grant D43TW001130-08, U01HL130010 (E.L.A.), UM1HG009375 (E.L.A), 5K22AI113060 (O.S.A.), 1R21AI123937 (O.S.A.), and R00DC012069 (C.S.M.); Defence Advanced Research Project Agency: HR0011-17-2-0047 (O.S.A.). Other support was provided by Jane Coffin Childs Memorial Fund (B.J.M.), Center for Theoretical Biological Physics postdoctoral fellowship (O.D.), Robertson Foundation (L.Z.), and McNair & Welch (Q-1866) Foundations (E.L.A.), French Government's Investissement d'Avenir program, Laboratoire d'Excellence Integrative Biology of Emerging Infectious Diseases (grant ANR-10-LABX-62-IBEID to L.L.), Agence Nationale de la Recherche grant ANR-17-ERC2-0016-01 (L.L.), European Union's Horizon 2020 research and innovation program under ZikaPLAN grant agreement no. 734584 (L.L.), Pew and Searle Scholars Programs (C.S.M.), Klingenstein-Simons Fellowship in the Neurosciences (C.S.M.). A.M.W., B.J.W., J.E.C. and S.N.M. were supported by Verily Life Sciences. L.B.V. is an investigator of the Howard Hughes Medical Institute.
Published: 2018

6. Gearing up to handle the mosaic nature of life in the quest for orthologs

Author: Forslund, Kristoffer, Pereira, Cécile, Capella-Gutiérrez, Salvador, da Silva, Alan Sousa, Altenhoff, Adrian, Huerta-Cepas, Jaime, Muffato, Matthieu, Patricio, Mateus, Vandepoele, Klaas, Ebersberger, Ingo, Blake, Judith, Fernández Breis, Jesualdo Tomás, Boeckmann, Brigitte, Gabaldon, Toni, Sonnhammer, Erik, Dessimoz, Christophe, Lewis, Suzanna, Bello, Carla, Briois, Sébastien, Chalstrey, Edward, Chiba, Hirokazu, Conchillo-Solé, Oscar, Daubin, Vincent, DeLuca, Todd, Dufayard, Jean-François, Durand, Dannie, Fernández-Breis, Jesualdo Tomás, Glover, Natasha, Hauser, Alexander, Heller, Davide, Kaduk, Mateus, Koch, Jan, Koonin, Eugene, Kriventseva, Evgenia, Kuraku, Shigehiro, Lecompte, Odile, Lespinet, Olivier, Levy, Jeremy, Liebeskind, Benjamin, Linard, Benjamin, Marcet-Houben, Marc, Kauffmann, Martin, McWhite, Claire, Mekhedov, Sergei, Moretti, Sebastien, Müller, Steven, Nadia, El-Mabrouk, Notredame, Cedric, Penel, Simon, Pilizota, Ivana, Redestig, Henning, Robinson-Rechavi, Marc, Schreiber, Fabian, Sjölander, Kimmen, Škunca, Nives, Steinegger, Martin, Szklarczyk, Damian, Thomas, Paul, Thuer, Ernst, Train, Clément, Uchiyama, Ikuo, Wittwer, Lucas, Xenarios, Ioannis, Yates, Bethan, Zdobnov, Evgeny, Waterhouse, Robert, European Molecular Biology Laboratory [Heidelberg] (EMBL), University of Florida [Gainesville], Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Bioinformatique (LRI) (BioInfo - LRI), Laboratoire de Recherche en Informatique (LRI), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Universitat Pompeu Fabra [Barcelona], Swiss Institute of Bioinformatics (SIB), Centre for Genomic Regulation (CRG), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, VIB Department of Plant Systems Biology, Ghent University [Belgium] (UGENT), Senckenberg Climate and Research, Applied Bioinformatics, University of Southern California (USC), Department of Computer Science, Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération (LBCMCP), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Harvard Medical School [Boston] (HMS), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Universidad de Murcia, National Center for Biotechnology Information (NCBI), University of Geneva Medical School, Genome Resource and Analysis Unit (GRAS), RIKEN Center for Developmental Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Swiss Institute of Bioinformatics, Comparative Bioinformatics, Department of Ecology and Evolution, Université de Lausanne (UNIL), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Universität Zürich [Zürich] (UZH), Defence Science and Technology Laboratory (Dstl), Ministry of Defence (UK) (MOD), Swiss Institute of Bioinformatics [Genève] (SIB), Medical School, Université de Genève (UNIGE), University of Florida [Gainesville] (UF), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Universitat Pompeu Fabra [Barcelona] (UPF), Swiss Institute of Bioinformatics [Lausanne] (SIB), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Department of Ecology and Evolution [Lausanne], Universität Zürich [Zürich] = University of Zurich (UZH), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Université de Lausanne = University of Lausanne (UNIL), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Genève = University of Geneva (UNIGE), European Molecular Biology Laboratory [Heidelberg] ( EMBL ), University of Florida [Gainesville] ( UF ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Bioinformatique (LRI) ( BioInfo - LRI ), Laboratoire de Recherche en Informatique ( LRI ), Université Paris-Sud - Paris 11 ( UP11 ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -CentraleSupélec-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -CentraleSupélec-Centre National de la Recherche Scientifique ( CNRS ), Centre for Genomic Regulation ( CRG ), European Bioinformatics Institute [Hinxton] ( EMBL-EBI ), European Molecular Biology Laboratory [Hinxton], Ghent University [Belgium] ( UGENT ), Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Southern California ( USC ), Swiss Federal Institute of Technology in Zürich ( ETH Zürich ), LBCMCP, Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Biométrie et Biologie Evolutive ( LBBE ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ), Harvard Medical School [Boston] ( HMS ), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales ( UMR AGAP ), Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), National Center for Biotechnology Information ( NCBI ), Genome Resource and Analysis Unit ( GRAS ), Institut de Génétique et de Biologie Moléculaire et Cellulaire ( IGBMC ), Université de Strasbourg ( UNISTRA ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Méthodes et Algorithmes pour la Bioinformatique ( MAB ), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier ( LIRMM ), Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Université de Lausanne ( UNIL ), University of California [Berkeley], Universität Zürich [Zürich] ( UZH ), Defence Science and Technology Laboratory ( Dstl ), Ministry of Defence (UK) ( MOD ), Swiss Institute of Bioinformatics [Genève] ( SIB ), Université de Genève ( UNIGE ), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: [ INFO.INFO-BI ] Computer Science [cs]/Bioinformatics [q-bio.QM], [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], ComputingMilieux_MISCELLANEOUS
Abstract: International audience; The Quest for Orthologs (QfO) is an open collaboration framework for experts in comparative phylogenomics and related research areas who have an interest in highly accurate orthology predictions and their applications. We here report highlights and discussion points from the QfO meeting 2015 held in Barcelona. Achievements in recent years have established a basis to support developments for improved orthology prediction and to explore new approaches. Central to the QfO effort is proper benchmarking of methods and services, as well as design of standardized datasets and standardized formats to allow sharing and comparison of results. Simultaneously, analysis pipelines have been improved, evaluated and adapted to handle large datasets. All this would not have occurred without the long-term collaboration of Consortium members. Meeting regularly to review and coordinate complementary activities from a broad spectrum of innovative researchers clearly benefits the community. Highlights of the meeting include addressing sources of and legitimacy of disagreements between orthology calls, the context dependency of orthology definitions, special challenges encountered when analyzing very anciently rooted orthologies, orthology in the light of whole-genome duplications, and the concept of orthologous versus paralogous relationships at different levels, including domain-level orthology. Furthermore, particular needs for different applications (e.g. plant genomics, ancient gene families and others) and the infrastructure for making orthol-ogy inferences available (e.g. interfaces with model organism databases) were discussed, with several ongoing efforts that are expected to be reported on during the upcoming 2017 QfO meeting.
Published: 2018

7. Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification

Author: Adriaenssens, Evelien, Roux, Simon, Brister, J. Rodney, Karsch-Mizrachi, Ilene, Kuhn, Jens, Varsani, Arvind, Yigang, Tong, Reyes, Alejandro, Lood, Cédric, Lefkowitz, Elliot, Sullivan, Matthew, Edwards, Robert, Simmonds, Peter, Rubino, Luisa, Sabanadzovic, Sead, Krupovic, Mart, Dutilh, Bas, Quadram Institute, Biotechnology and Biological Sciences Research Council (BBSRC), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), National Center for Biotechnology Information (NCBI), Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), Arizona State University [Tempe] (ASU), University of Cape Town, Beijing University of Chemical Technology, Universidad de los Andes [Bogota] (UNIANDES), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], University of Alabama at Birmingham [ Birmingham] (UAB), Ohio State University [Columbus] (OSU), Flinders University [Adelaide, Australia], University of Oxford, CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] (IPSP), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Mississippi State University [Mississippi], Virologie des archées - Archaeal Virology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Utrecht University [Utrecht], E.M.A. gratefully acknowledges the support of the Biotechnology and Biological Sciences Research Council (BBSRC), and this research was funded by the BBSRC Institute Strategic Program Gut Microbes and Health BB/R012490/1 and its constituent projects BBS/E/F/000PR10353 and BBS/E/F/000PR10356. The work conducted by the US Department of Energy (DOE) Joint Genome Institute (S.R.) was supported by the Office of Science of the DOE under contract no. DE-AC02-05CH11231. Work by J.R.B. and I.K.M. was supported by the National Center for Biotechnology Information of the National Library of Medicine (NLM), NIH. This work was supported in part through Laulima Government Solutions, LLC, prime contract with the NIAID under contract no. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC, under Contract No. HHSN272201800013C. M.B.S. was supported by the US National Science Foundation Award #1759874. R.A.E. was supported by the National Institute of Diabetes and Digestive and Kidney Diseases of the NIH under award no. RC2DK116713 and by the Australian Research Council under award no. DP220102915. C.L. was supported by a Postdoctoral Mandate from KU Leuven (PDMt2/21/038) and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC 2051 – Project-ID 390713860. E.J.L. was supported by the NIAID, NIH, under award no. U24AI162625. P.S. was supported by a Wellcome Trust Biomedical Resource grant (WT108418AIA). S.S. acknowledges support from the Mississippi Agricultural and Forestry Experiment Station (MAFES), US Department of Agriculture (USDA)–Agricultural Research Service project 58-6066-9-033, and the National Institute of Food and Agriculture, USDA, Hatch Project, under accession USDA 1021494. B.E.D. was supported by the European Research Council (ERC) Consolidator Grant 865694: DiversiPHI, the DFG under Germany’s Excellence Strategy – EXC 2051 – Project-ID 390713860, the Alexander von Humboldt Foundation in the context of an Alexander von Humboldt Professorship founded by German Federal Ministry of Education and Research, and the European Union’s Horizon 2020 research and innovation program, under Marie Skłodowska-Curie Actions Innovative Training Networks grant agreement no. 955974 (VIROINF).
Subjects: [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology
Published: 2023

8. Plant virus movement proteins originated from jelly-roll capsid proteins

Author: Butkovic, Anamarija, Dolja, Valerian, Koonin, Eugene, Krupovic, Mart, Virologie des archées - Archaeal Virology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Oregon State University (OSU), National Center for Biotechnology Information (NCBI), and ANR-21-CE11-0001,ArcFus,Protéines de classe II de fusion membranaire chez les archées(2021)
Subjects: [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology
Abstract: International audience; Numerous, diverse plant viruses encode movement proteins (MPs) that aid the virus movement through plasmodesmata, the plant intercellular channels. MPs are essential for virus spread and propagation in distal tissues, and several unrelated MPs have been identified. The 30K superfamily of MPs (named after the molecular mass of tobacco mosaic virus MP, the classical model of plant virology) is the largest and most diverse MP variety, represented in 16 virus families, but its evolutionary origin remained obscure. Here, we show that the core structural domain of the 30K MPs is homologous to the jelly-roll domain of the capsid proteins (CPs) of small RNA and DNA viruses, in particular, those infecting plants. The closest similarity was observed between the 30K MPs and the CPs of the viruses in the families Bromoviridae and Geminiviridae . We hypothesize that the MPs evolved via duplication or horizontal acquisition of the CP gene in a virus that infected an ancestor of vascular plants, followed by neofunctionalization of one of the paralogous CPs, potentially through the acquisition of unique N- and C-terminal regions. During the subsequent coevolution of viruses with diversifying vascular plants, the 30K MP genes underwent explosive horizontal spread among emergent RNA and DNA viruses, likely permitting viruses of insects and fungi that coinfected plants to expand their host ranges, molding the contemporary plant virome.
Published: 2023

9. The virome of the last eukaryotic common ancestor and eukaryogenesis

Author: Mart Krupovic, Valerian V. Dolja, Eugene V. Koonin, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris] (IP), Oregon State University (OSU), National Center for Biotechnology Information (NCBI), E.V.K. is supported by funds from the Intramural Research Program of the National Institutes of Health (National Library of Medicine). V.V.D. was partially supported by a National Institutes of Health/National Library of Medicine/National Center for Biotechnology Information Visiting Scientist Fellowship. M.K. was supported by l’Agence Nationale de la Recherche grant ANR-21-CE11-0001-01., ANR-20-CE20-0009,VIROMET,Devoiler le virome des archées methanogenes(2020), and ANR-21-CE11-0001,ArcFus,Protéines de classe II de fusion membranaire chez les archées(2021)
Subjects: Microbiology (medical), Immunology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Genetics, Cell Biology, Applied Microbiology and Biotechnology, Microbiology
Abstract: International audience; All extant eukaryotes descend from the last eukaryotic common ancestor (LECA), which is thought to have featured complex cellular organization. To gain insight into LECA biology and eukaryogenesis-the origin of the eukaryotic cell, which remains poorly understood-we reconstructed the LECA virus repertoire. We compiled an inventory of eukaryotic hosts of all major virus taxa and reconstructed the LECA virome by inferring the origins of these groups of viruses. The origin of the LECA virome can be traced back to a small set of bacterial-not archaeal-viruses. This provenance of the LECA virome is probably due to the bacterial origin of eukaryotic membranes, which is most compatible with two endosymbiosis events in a syntrophic model of eukaryogenesis. In the first endosymbiosis, a bacterial host engulfed an Asgard archaeon, preventing archaeal viruses from entry owing to a lack of archaeal virus receptors on the external membranes.
Published: 2023

10. Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein

Author: Anamarija Butkovic, Simona Kraberger, Zoe Smeele, Darren P Martin, Kara Schmidlin, Rafaela S Fontenele, Michelle R Shero, Roxanne S Beltran, Amy L Kirkham, Maketalena Aleamotu’a, Jennifer M Burns, Eugene V Koonin, Arvind Varsani, Mart Krupovic, Virologie des archées - Archaeal Virology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Arizona State University [Tempe] (ASU), University of Cape Town, Woods Hole Oceanographic Institution (WHOI), University of California [Santa Cruz] (UC Santa Cruz), University of California (UC), US Fish and Wildlife Service, Newcastle University [Newcastle], Texas Tech University [Lubbock] (TTU), National Center for Biotechnology Information (NCBI), A.B. was supported by a post-doctoral fellowship from Foundation pour la Recherche Mèdicale (grant number SPF202110014092). M.K. was supported by a grant from the l’Agence Nationale de la Recherche (ANR-20-CE20-0009-02). A.L.K. and R.S.B. were supported by Institutional Development Awards (IDeA) Networks of Biomedical Research Excellence Assistantships (grant number P20GM103395) from the National Institute of General Medical Sciences of the National Institutes of Health (NIH). E.V.K. was supported by the Intramural Research Program of the NIH (National Library of Medicine).Weddell seal samples were collected under National Marine Fisheries Service Marine Mammal permit #17411, Antarctic Conservation Act permit #2014-003, and the University of Alaska Anchorage and University of Alaska Fairbanks’s Institutional Animal Care and Use Committee approvals #419971 and #854089, with funding from the National Science Foundation grant ANT-1246463 to J.M.B.The molecular work described in this study is supported by the Center of Evolution and Medicine Venture Fund (Center of Evolution and Medicine, Arizona State University, USA) grant awarded to A.V., and ANR-20-CE20-0009,VIROMET,Devoiler le virome des archées methanogenes(2020)
Subjects: virus evolution, Commensaviricota, jelly-roll fold, Virology, structural modelling, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, taxonomy and classification, Anellovirus, Microbiology, capsid proteins
Abstract: Anelloviruses are highly prevalent in diverse mammals, including humans, but so far have not been linked to any disease and are considered to be part of the ‘healthy virome’. These viruses have small circular single-stranded DNA (ssDNA) genomes and encode several proteins with no detectable sequence similarity to proteins of other known viruses. Thus, anelloviruses are the only family of eukaryotic ssDNA viruses currently not included in the realm Monodnaviria. To gain insights into the provenance of these enigmatic viruses, we sequenced more than 250 complete genomes of anelloviruses from nasal and vaginal swab samples of Weddell seal (Leptonychotes weddellii) from Antarctica and a fecal sample of grizzly bear (Ursus arctos horribilis) from USA, and performed a comprehensive family-wide analysis of the signature anellovirus protein, ORF1. Using state-of-the-art remote sequence similarity detection approaches and structural modeling with AlphaFold2, we show that ORF1 orthologs from all Anelloviridae genera adopt a jelly-roll fold typical of viral capsid proteins, establishing an evolutionary link to other eukaryotic ssDNA viruses, specifically, circoviruses. However, unlike capsid proteins of other ssDNA viruses, ORF1 encoded by anelloviruses from different genera display remarkable variation in size, due to insertions into the jelly-roll domain. In particular, the insertion between β-strands H and I forms a projection domain predicted to face away from the capsid surface and function at the interface of virus-host interactions. Consistent with this prediction and supported by recent experimental evidence, the outermost region of the projection domain is a mutational hotspot, where rapid evolution was likely precipitated by the host immune system. Collectively, our findings further expand the known diversity of anelloviruses and explain how anellovirus ORF1 proteins likely diverged from canonical jelly-roll capsid proteins through gradual augmentation of the projection domain. We suggest assigning Anelloviridae to a new phylum, ‘Commensaviricota’, and including it into kingdom Shotokuvirae (realm Monodnaviria), alongside Cressdnaviricota and Cossaviricota.
Published: 2023

11. Bipartite Network Analysis of the Archaeal Virosphere: Evolutionary Connections between Viruses and Capsidless Mobile Elements

Author: Eugene V. Koonin, Jaime Iranzo, David Prangishvili, Mart Krupovic, National Center for Biotechnology Information (NCBI), Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), Institut Pasteur [Paris], National Center for Biotechnology Information ( NCBI ), and Biologie Moléculaire du Gène chez les Extrêmophiles ( BMGE )
Subjects: 0301 basic medicine, Archaeal Viruses, viruses, royalty, Genome, MESH : Archaea, MESH : Biological Evolution, Bacteriophages, Gene Regulatory Networks, Phylogeny, Genetics, Phylogenetic tree, Turriviridae, Biological Evolution, MESH : Bacteriophages, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, MESH : DNA Transposable Elements, MESH : Genome, Viral, Plasmids, Immunology, Genome, Viral, Biology, [ SDV.MP.VIR ] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Microbiology, 03 medical and health sciences, royalty.royal_line, Caudovirales, Phylogenetics, Virology, MESH : Virion, MESH : Bacteria, Human virome, [ SDV ] Life Sciences [q-bio], Bacteria, Virion, MESH : Phylogeny, Computational Biology, biology.organism_classification, Archaea, MESH : Archaeal Viruses, 030104 developmental biology, Genetic Diversity and Evolution, Evolutionary biology, MESH : Plasmids, MESH : Gene Regulatory Networks, Insect Science, DNA Transposable Elements, Bacterial virus, MESH : Computational Biology
Abstract: Archaea and particularly hyperthermophilic crenarchaea are hosts to many unusual viruses with diverse virion shapes and distinct gene compositions. As is typical of viruses in general, there are no universal genes in the archaeal virosphere. Therefore, to obtain a comprehensive picture of the evolutionary relationships between viruses, network analysis methods are more productive than traditional phylogenetic approaches. Here we present a comprehensive comparative analysis of genomes and proteomes from all currently known taxonomically classified and unclassified, cultivated and uncultivated archaeal viruses. We constructed a bipartite network of archaeal viruses that includes two classes of nodes, the genomes and gene families that connect them. Dissection of this network using formal community detection methods reveals strong modularity, with 10 distinct modules and 3 putative supermodules. However, compared to similar previously analyzed networks of eukaryotic and bacterial viruses, the archaeal virus network is sparsely connected. With the exception of the tailed viruses related to bacteriophages of the order Caudovirales and the families Turriviridae and Sphaerolipoviridae that are linked to a distinct supermodule of eukaryotic and bacterial viruses, there are few connector genes shared by different archaeal virus modules. In contrast, most of these modules include, in addition to viruses, capsidless mobile elements, emphasizing tight evolutionary connections between the two types of entities in archaea. The relative contributions of distinct evolutionary origins, in particular from nonviral elements, and insufficient sampling to the sparsity of the archaeal virus network remain to be determined by further exploration of the archaeal virosphere. IMPORTANCE Viruses infecting archaea are among the most mysterious denizens of the virosphere. Many of these viruses display no genetic or even morphological relationship to viruses of bacteria and eukaryotes, raising questions regarding their origins and position in the global virosphere. Analysis of 5,740 protein sequences from 116 genomes allowed dissection of the archaeal virus network and showed that most groups of archaeal viruses are evolutionarily connected to capsidless mobile genetic elements, including various plasmids and transposons. This finding could reflect actual independent origins of the distinct groups of archaeal viruses from different nonviral elements, providing important insights into the emergence and evolution of the archaeal virome.
Published: 2016

12. The global virome: How much diversity and how many independent origins?

Author: Eugene V. Koonin, Mart Krupovic, Valerian V. Dolja, National Center for Biotechnology Information (NCBI), Virologie des archées - Archaeal Virology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Oregon State University (OSU), and Eugene V. Koonin is supported by the funds of the Intramural Research Program of the National Institutes of Health of the USA. Valerian V. Dolja was partially supported by NIH/NLM/NCBI Visiting Scientist Fellowship.
Subjects: [SDV]Life Sciences [q-bio], Microbiology, Ecology, Evolution, Behavior and Systematics
Abstract: International audience; Viruses are considered to be the most abundant biological entities on earth. They also display striking genetic diversity as emphatically demonstrated by the recent advances of metagenomics and metatranscriptomics. But what are the limits of this diversity, that is, how many virus species in the earth virome? By combining the available estimates of the number of prokaryote species with those of the virome size, we obtain back-of-the-envelope estimates of the total number of distinct virus species, which come out astronomically large, from about 10^7 to about 10^9 . The route of virus origins apparently involved non-viral replicators capturing and exapting various cellular proteins to become virus capsid subunits. How many times in the history of life has this happened? In other words, how many realms of viruses, the highest rank taxa that are supposed to be monophyletic, comprise the global virome? We argue that viruses emerged on a number (even if far from astronomical) independent occasions, so the number of realms will considerably increase from the current 6, by splitting some of the current realms, giving the realm status to some of the currently unclassified groups of viruses and discovery of new distinct groups.
Published: 2023

13. Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee

Author: Dann Turner, Andrey N. Shkoporov, Cédric Lood, Andrew D. Millard, Bas E. Dutilh, Poliane Alfenas-Zerbini, Leonardo J. van Zyl, Ramy K. Aziz, Hanna M. Oksanen, Minna M. Poranen, Andrew M. Kropinski, Jakub Barylski, J Rodney Brister, Nina Chanisvili, Rob A. Edwards, François Enault, Annika Gillis, Petar Knezevic, Mart Krupovic, Ipek Kurtböke, Alla Kushkina, Rob Lavigne, Susan Lehman, Malgorzata Lobocka, Cristina Moraru, Andrea Moreno Switt, Vera Morozova, Jesca Nakavuma, Alejandro Reyes Muñoz, Jānis Rūmnieks, BL Sarkar, Matthew B. Sullivan, Jumpei Uchiyama, Johannes Wittmann, Tong Yigang, Evelien M. Adriaenssens, UCL - SST/ELI/ELIM - Applied Microbiology, University of the West of England [Bristol] (UWE Bristol), University College Cork (UCC), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), University of Leicester, Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], Utrecht University [Utrecht], Universidade Federal de Viçosa = Federal University of Viçosa (UFV), University of the Western Cape (UWC), Cairo University, Helsingin yliopisto = Helsingfors universitet = University of Helsinki, University of Guelph, Adam Mickiewicz University in Poznań (UAM), National Center for Biotechnology Information (NCBI), George Eliava Institute of Bacteriophages, Microbiology and Virology [Tbilisi, Georgia], Flinders Accelerator for Microbiome Exploration [Adelaide, Australia], Laboratoire Microorganismes : Génome et Environnement (LMGE), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), Université Catholique de Louvain = Catholic University of Louvain (UCL), University of Novi Sad, Virologie des archées - Archaeal Virology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of the Sunshine Coast (USC), D.K. Zabolotny Institute of Microbiology and Virology [Kyiv, Ukraine], National Academy of Sciences of Ukraine (NASU), University of Gdańsk (UG), Center for Biologics Evaluation and Research, U.S. Food and Drug Administration (FDA), Institute of Biochemistry and Biophysics [Warsaw] (IBB), University of Oldenburg, Pontificia Universidad Católica de Chile (UC), Institute of Chemical Biology and Fundamental Medicine [Novosibirsk, Russia] (ICBFM SB RAS), Siberian Branch of the Russian Academy of Sciences (SB RAS), Makerere University [Kampala, Ouganda] (MAK), Universidad de los Andes [Bogota] (UNIANDES), Latvian Biomedical Research and Study Center (BMC), National Institute of Cholera and Enteric Diseases, Ohio State University [Columbus] (OSU), Okayama University, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ), Beijing University of Chemical Technology, Quadram Institute Bioscience [Norwich, U.K.] (QIB), Biotechnology and Biological Sciences Research Council (BBSRC), B.E.D. was supported by the European Research Council (ERC) Consolidator Grant 865694: DiversiPHI, the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy – EXC 2051 – Project-ID 390713860, the Alexander von Humboldt Foundation in the context of an Alexander von Humboldt Professorship funded by the German Federal Ministry of Education and Research, and the European Union’s Horizon 2020 Research and Innovation Program, under the Marie Skłodowska-Curie Actions Innovative Training Networks grant agreement no. 955974 (VIROINF). Work by J.R.B. was supported by the National Center for Biotechnology Information of the National Library of Medicine (NLM), National Institutes of Health. R.A.E was supported by an award from the National Institute of Diabetes and Digestive and Kidney Diseases of the National Institute of Health RC2DK116713 and an award from the Australian Research Council, DP220102915. R.L. is supported by the research grant PHAGEFORCE from the KU Leuven. C.L. is supported by the Research Foundation - Flanders (FWO Grant 12D8623N) and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy – EXC 2051 – Project-ID 390713860. V.M. is supported by the Russian state-funded project For ICBFM SB RAS, Grant 121031300043-8. H.M.O. was supported by the University of Helsinki and Academy of Finland by funding for FINStruct and Instruct Centre Finland, Instruct-ERIC. M.M.P. acknowledges funding from the Sigrid Jusélius Foundation and the Academy of Finland (grant 331627). A.N.S is supported by a Wellcome Trust Research Career Development Fellowship [220646/Z/20/Z] and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No 101001684). E.M.A. gratefully acknowledges funding by the Biotechnology and Biological Sciences Research Council (BBSRC), this research was funded by the BBSRC Institute Strategic Programme Gut Microbes and Health BB/R012490/1 and its constituent projects BBS/E/F/000PR10353 and BBS/E/F/000PR10356., European Project: 865694,H2020-EU.1.1. - EXCELLENT SCIENCE - European Research Council (ERC),DiversiPHI(2020), and European Project: 101001684,ERC-2020-COG,PHAGENET(2021)
Subjects: Science & Technology, [SDV]Life Sciences [q-bio], Virology, General Medicine, Life Sciences & Biomedicine
Abstract: This article summarises the activities of the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses for the period of March 2021−March 2022. We provide an overview of the new taxa proposed in 2021, approved by the Executive Committee, and ratified by vote in 2022. Significant changes to the taxonomy of bacterial viruses were introduced: the paraphyletic morphological families Podoviridae, Siphoviridae, and Myoviridae as well as the order Caudovirales were abolished, and a binomial system of nomenclature for species was established. In addition, one order, 22 families, 30 subfamilies, 321 genera, and 862 species were newly created, promoted, or moved.
Published: 2023

14. Findings of the WMT 2022 Biomedical Translation Shared Task: Monolingual Clinical Case Reports

Author: Neves, M., Yepes, A. J., Siu, A., Roller, R., Thomas, P., Navarro, M. V., Yeganova, L., Wiemann, D., Di Nunzio, G. M., Vezzani, F., Gerardin, C., Bawden, R., Estrada, D. J., Lima-López, S., Farré-Maduell, E., Krallinger, M., Grozea, C., Névéol, A., German Centre for the Protection of Laboratory Animals (Bf3R), Royal Melbourne Institute of Technology University (RMIT University), Berliner Hochschule für Technik (BHT), Deutsches Forschungszentrum für Künstliche Intelligenz GmbH = German Research Center for Artificial Intelligence (DFKI), Leica Biosystems, National Center for Biotechnology Information (NCBI), Novartis Pharma AG, Università di studi di Padova - Dipartimento di studi linguistici e letterari (UP DISLL), Università degli Studi di Padova = University of Padua (Unipd), Azienda Ospedale Università di Padova = Hospital-University of Padua (AOUP), Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Automatic Language Modelling and ANAlysis & Computational Humanities (ALMAnaCH), Inria de Paris, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Fraunhofer Institute for Open Communication Systems (Fraunhofer FOKUS), Fraunhofer (Fraunhofer-Gesellschaft), Information, Langue Ecrite et Signée (ILES), Laboratoire Interdisciplinaire des Sciences du Numérique (LISN), Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Sciences et Technologies des Langues (STL), Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), and ANR-19-P3IA-0001,PRAIRIE,PaRis Artificial Intelligence Research InstitutE(2019)
Subjects: [INFO.INFO-CL]Computer Science [cs]/Computation and Language [cs.CL]
Abstract: International audience; In the seventh edition of the WMT Biomedical Task, we addressed a total of seven language pairs, namely English/German, English/French, English/Spanish, English/Portuguese, English/Chinese, English/Russian, English/Italian. This year’s test sets covered three types of biomedical text genre. In addition to scientific abstracts and terminology items used in previ- ous editions, we released test sets of clinical cases. The evaluation of clinical cases translations were given special attention by involving clinicians in the preparation of reference translations and manual evaluation. For the main MEDLINE test sets, we received a total of 609 submissions from 37 teams. For the ClinSpEn sub-task, we had the participation of five teams.
Published: 2022

15. Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

Author: Dirk Redecker, Johannes Z. Groenewald, B. Stielow, Ibai Olariaga, Wendy A. Untereiner, Steven D. Leavitt, Scott Federhen, Samantha C. Karunarathna, Pedro W. Crous, Katerina Fliegerova, Jianping Xu, Ana Crespo, M. Teresa Telleria, Soili Stenroos, Martha J. Powell, Sajeewa S. N. Maharachchikumbura, Gianluigi Cardinali, Laszlo Irinyi, Hiran A. Ariyawansa, Javier Diéguez Uribeondo, Andrew M. Minnis, Paul M. Kirk, Zai-Wei Ge, Duong Vu, Richard C. Hamelin, Conrad L. Schoch, Jian-Kui Liu, Wieland Meyer, Kevin D. Hyde, Csaba Vágvölgyi, Bryn T. M. Dentinger, Ning Zhang, Dhanushka Udayanga, Tamás Petkovits, Qing Cai, Cletus P. Kurtzman, Raquel Pino-Bodas, Jie Chen, Michael Weiß, Karl-Henrik Larsson, Leho Tedersoo, María P. Martín, Peter M. Letcher, Gábor M. Kovács, Liang-Dong Guo, Kazuaki Tanaka, Bhushan Shrestha, Andrew N. Miller, Krishna V. Subbarao, Nicolas Feau, Urmas Kõljalg, Huzefa A. Raja, D. Jean Lodge, Karen K. Nakasone, Jean-Marc Moncalvo, Nalin N. Wijayawardene, Sung-Oui Suh, Cécile Gueidan, Teun Boekhout, Wen Ying Zhuang, Marieka Gryzenhout, Jullie M. Sarmiento-Ramírez, Bart Buyck, H. Thorsten Lumbsch, Marizeth Groenewald, Seung-Beom Hong, Keith A. Seifert, Peter R. Johnston, Janet Jennifer Luangsa-ard, Barbara Robbertse, Kessy Abarenkov, Dimuthu S. Manamgoda, Z. Wilhelm de Beer, Pradeep K. Divakar, Tuula Niskanen, Patrik Inderbitzin, M. Catherine Aime, Bevan S. Weir, Sarah Hambleton, Zhu L. Yang, R. Henrik Nilsson, Kare Liimatainen, Cobus M. Visagie, Krisztina Krizsán, Michael J. Wingfield, Ulrike Damm, Gareth W. Griffith, Donald M. Walker, Tamás Papp, Vincent Robert, Miguel A. García, Valérie Hofstetter, Martin I. Bidartondo, Karen Hansen, Margarita Dueñas, Jos Houbraken, Karen W. Hughes, Kerstin Voigt, Giuseppina Mulè, Martin Grube, Ekaphan Kraichak, National Center for Biotechnology Information (NCBI), National Institutes of Health (NIH), NLM, National Institutes of Health, CBS-KNAW Fungal Biodiversity Centre, Department of Pharmaceutical Sciences – Microbiology, Università degli Studi di Perugia (UNIPG), Molecular Mycology Research Laboratory, University of Sydney, Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School-Westmead Hospital, The Westmead Institute for Medical Research, Faculty of Biological and Environmental Sciences [Helsinki], University of Helsinki, Ecology and Evolutionary Biology, University of Tennessee System, Illinois Natural History Survey, University of Illinois System-University of Illinois System, Mycology Section, Jodrell Laboratory, Royal Botanic Gardens, University of Tartu, Department of Botany and Plant Pathology, Oregon State University (OSU), Institute of Excellence in Fungal Research and School of Science, Mae Fah Luang University [Thaïlande] (MFU), Imperial College London, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Chinese Academy of Sciences [Beijing] (CAS), School of Science, Departamento de Biologia Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Museum of Natural History Görlitz, Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria (UPSpace), Real Jardin Botanico (RJB), Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia (UBC), Czech Academy of Sciences [Prague] (CAS), Department of Biology, Northern Arizona University [Flagstaff], Aberystwyth University, Institute of Plant Sciences, Karl Franzens University, Department of Plant Sciences, University of California, Plant Industry, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences [Changchun Branch] (CAS), Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food [Ottawa] (AAFC), Department of Botany, National University of Ireland [Galway] (NUI Galway), Département de recherche en Protection des végétaux grandes cultures et vigne/Viticulture et oenologie, Agroscope, Korean Agricultural Culture Collection, National Academy of Agricultural Science, Davis Department of Plant Pathology, Manaaki Whenua – Landcare Research [Lincoln], Institute of Biology, Department of Plant Anatomy, Eötvös Loránd University (ELTE), Plant Protection Institute [Budapest] (ATK NOVI), Centre for Agricultural Research [Budapest] (ATK), Hungarian Academy of Sciences (MTA)-Hungarian Academy of Sciences (MTA), Science and Education, Field Museum, Department of Microbiology [Szeged], University of Szeged [Szeged], Bacterial Foodborne Pathogens and Mycology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research (NCAUR), United States Department of Agriculture (USDA)-United States Department of Agriculture (USDA), The Natural History Museum [London] (NHM), Department of Biological Sciences, The Open University [Milton Keynes] (OU), Plant Biology, Department of Biosciences, Forest Service, United States Department of Agriculture, Biotec - National Center for Genetic Engineering and Biotechnology, Department of Medical Microbiology and Immunology [Göteborg], University of Gothenburg (GU), Department of Natural History, Royal Ontario Museum, Department of Ecology Evolutionary Biology, University of Toronto, Institute of Sciences of Food Production (ISPA), Consiglio Nazionale delle Ricerche (CNR), Northern Research Station, U.S. Forest Service, Center for Forest Mycology Research (CFMR), Botany Unit, Finnish Museum of Natural History, Finnish Museum of Natural History (LUOMUS), University of Helsinki-University of Helsinki, Department of Chemistry and Biochemistry, University of California [Los Angeles] (UCLA), University of California-University of California, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institute of Life Science and Biotechnology, Sungkyunkwan University [Suwon] (SKKU), Mycology and Botany Program, American Type Culture Collection (ATCC), Faculty of Agriculture and Life Science, University of Maribor, Natural History Museum, University of Kansas [Lawrence] (KU), University of California [Davis] (UC Davis), Jena Microbial Resource Collection, Leibniz Institute for Natural Product Research and Infection Biology (Hans Knoell Institute), Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], Department of Natural Sciences, University of Findlay, Institute of Evolution and Ecology, Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, McMaster University, Kunming Institute of Botany [CAS] (KIB), Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey [New Brunswick] (RU), Rutgers University System (Rutgers)-Rutgers University System (Rutgers), National Center for Biotechnology Information, National Library of Medicine, Schoch, Conrad L., Département Systématique et Evolution, Muséum national d'Histoire naturelle (MNHN), Chinese Academy of Sciences, Kunming Institute of Botany, Universidad Complutense de Madrid [Madrid] (UCM), Czech Academy of Sciences [Prague] (ASCR), Landcare Research, United States Department of Agriculture - USDA (USA)-United States Department of Agriculture - USDA (USA), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Friedrich-Schiller-Universität Jena, Eberhard Karls Universität Tübingen, National Center for Biotechnology Information ( NCBI ), National Institutes of Health ( NIH ), Università degli Studi di Perugia, Westmead Institute for Medical Research, Department of Biological and Environmental Sciences, University of Tennessee, Oregon State University ( OSU ), Mae Fah Luang University [Thaïlande] ( MFU ), Muséum National d’Histoire Naturelle ( MNHN ), Universidad Complutense de Madrid [Madrid] ( UCM ), Forestry and Agricultural Biotechnology Institute ( FABI ), University of Pretoria ( UPSpace ), Real Jardin Botanico ( RJB ), University of British Columbia ( UBC ), Czech Academy of Sciences [Prague] ( ASCR ), Commonwealth Scientific and Industrial Research Organisation [Canberra] ( CSIRO ), Chinese Academy of Sciences [Changchun Branch] ( CAS ), Agriculture and Agri-Food Canada ( AAFC ), National University of Ireland [Galway] ( NUI Galway ), Eotvos Lorand University, Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences [Budapest], National Center for Agricultural Utilization Research, The Open University [Milton Keynes] ( OU ), University of Gothenburg ( GU ), Institute of Sciences of Food Production, Center for Forest Mycology Research ( CFMR ), Botanical Museum, Finnish Museum of Natural History, University of California at Los Angeles [Los Angeles] ( UCLA ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté ( UBFC ), Sungkyunkwan University, American Type Culture Collection ( ATCC ), University of Kansas [Lawrence] ( KU ), University of California Davis, Leibniz Institute for Natural Product Research and Infection Biology, Rutgers University (State University of New Jersey), Università degli Studi di Perugia = University of Perugia (UNIPG), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), University of Pretoria [South Africa], University of California (UC), Agriculture and Agri-Food (AAFC), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, and University of California (UC)-University of California (UC)
Subjects: [SDV]Life Sciences [q-bio], sequence analyses, ribosomal dna, Intergenic region, 0807 Library And Information Studies, Databases, Genetic, RefSeq, Cluster Analysis, donnée de séquence moléculaire, DNA, Fungal, Genetics, DNA, Intergenic, Genes, Fungal, Molecular Sequence Annotation, Fungi, Sequence Analysis, DNA, Medicine (all), Phylogenetic tree, EPS-4, 3. Good health, internal transcribed spacer, Fungal, Identification (biology), Original Article, General Agricultural and Biological Sciences, Life Sciences & Biomedicine, Sequence Analysis, Information Systems, specimen, life, Sequence analysis, arbuscular mycorrhizal fungi, interspecific hybridization, Computational biology, Biology, General Biochemistry, Genetics and Molecular Biology, DNA sequencing, Databases, Genetic, evolution, Internal transcribed spacer, species complex, Science & Technology, Intergenic, [ SDV ] Life Sciences [q-bio], barcode, 0804 Data Format, DNA, Laboratorium voor Phytopathologie, MATHEMATICAL & COMPUTATIONAL BIOLOGY, référence, Genes, Laboratory of Phytopathology, identification
Abstract: DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Reannotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi., B.R. and C.L.S. acknowledge support from the Intramural Research Program of the National Institutes of Health, National Library of Medicine
Published: 2014

16. A life LINE for large viruses

Author: Eugene V Koonin, Mart Krupovic, National Center for Biotechnology Information (NCBI), Virologie des archées - Archaeal Virology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), and Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: General Immunology and Microbiology, Retroelements, General Neuroscience, infectious disease, Poxviridae, evolutionary biology, microbiology, Vaccinia virus, General Medicine, Virus Replication, General Biochemistry, Genetics and Molecular Biology, retrotransposons, LINE-1, poxvirus, evolution, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, horizontal gene transfer, viruses, human
Abstract: International audience; As long suspected, poxviruses capture host genes through a reverse-transcription process now shown to be mediated by retrotransposons.
Published: 2022

17. D8.1 EOSC-Life Methodology framework to enhance reproducibility within EOSC-Life – revised version

Author: Bietrix, Florence, Carazo, José-Maria, Capella-Gutierrez, Salvador, Coppens, Frederik, Chiusano, Maria-Luisa, David, Romain, Fernandez Jose, Maria, Fratelli, Maddalena, Heriche, Jean-Karim, Goble, Carole, Gribbon, Philip, Holub, Petr, P.Joosten, Robbie, Leo, Simone, Owen, Stuart, Parkinson, Helen, Pieruschka, Roland, Pireddu, Luca, Porcu, Luca, Raess, Michael, Rodriguez-Navas, Laura, Scherer, Andreas, Soiland-Reyes, Stian, Tang, Jing, Saunders, Gary, European Advanced Translational Research Infrastructure (EATRIS), National Center for Biotechnology Information (NCBI), Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), University of Naples Federico II = Università degli studi di Napoli Federico II, European Research Infrastructure on Highly Pathogenic Agents (ERINHA-AISBL), IRCCS - Istituto di Ricerche Farmacologiche 'Mario Negri' [Milan, Italy], European Molecular Biology Laboratory [Heidelberg] (EMBL), University of Manchester [Manchester], ITMP Drug Discovery (ITMP), Czech Academy of Sciences [Prague] (CAS), Department of Computer Science, University of Manchester, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association, CRS4 Bioinformat, INFRAFRONTIER GmbH [Neuherberg], Department of Computer Science, The University of Manchester, TKK Helsinki University of Technology (TKK), Bietrix, Florence, Carazo, José Maria, Capella-Gutierrez, Salvador, Coppens, Frederik, Chiusano, Maria Luisa, David, Romain, Fernandez, Jose Maria, Fratelli, Maddalena, Heriche, Jean-Karim, Goble, Carole, Gribbon, Philip, Holub, Petr, P. Joosten, Robbie, Leo, Simone, Owen, Stuart, Parkinson, Helen, Pieruschka, Roland, Pireddu, Luca, Porcu, Luca, … Saunders, Gary. (2022). EOSC-Life Methodology framework to enhance reproducibility within EOSC-Life – revised version. Zenodo. https://doi.org/10.5281/zenodo.7137744, EOSC-Life, INFRAFRONTIER, VIB, EMBRC, ERINHA, IRFMN, EMBL-HD, UNIMAN, Fraunhofer, BBMRI-ERIC, NKI, EMBL-EBI, CSR4, HU, CSIC, BSC, and European Project: 824087,EOSC-Life
Subjects: Life science, Open Science, Framework Implementation, Data sharing, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Data sharing tools, research infrastructures, Reproducibility
Abstract: The original scope of task 8.3 is to develop a framework to assess the impact on reproducibility of the availability of life-science open data and workflows in the cloud.Such a framework should include the understanding of the tools and services produced and made available, the gaps they are filling up and their expected impact.A great part of the activities within EOSC-Life is actually related to reproducibility and provides in several ways tools that will have an impact. We describe here such activities and explain why and how they will have an impact on reproducibility in life sciences. In addition, for each action, we provide an indication of how we could measure its impact in practical ways, using adequate proxies. For these reasons, we changed the title of the deliverable, from “framework to assess ...” to “framework to enhance reproducibility”.First of all, we reasoned on what can be the contribution of open science to improve the reproducibility of research. Publicly sharing data, protocols, tools and computational workflows makes it possible to compare or combine the data and outcomes from different studies within a discipline as well as integrate data across scientific domains. It allows conclusions to be validated and possibly corrected as well as being reinforced by meta-analyses. Replication data and test/training data can also be used in many applications to contribute to reproducible research. Moreover, new hypotheses, different from the original aims of the study, can be explored. Datasets can be re-used to develop and test new methods, to conduct scientific and technical benchmarking activities and to support training activities. Therefore, in addition to generating more value from research investments, data sharing has the potential to increase confidence in research outcomes and increase knowledge dissemination. These benefits of open sharing have long been recognized in some fields such as bioinformatics, which has a long history of publicly sharing data with, for example, public repositories for nucleotide sequences going back 30 years and the Protein Data Bank (PDB), a repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies, that celebrates its 50th birthday this year.In this notion, any improvement in sharing of data, tools and workflows among scientists and across disciplines, which is the aim of EOSC-Life and the wider EOSC, will contribute to reproducible science. In addition to this general scope, several specific actions to frame transparency in the reporting of experimental protocols, data and analytical workflows warrant the reproducibility of every single object (experimental results, data, or workflows) that is made available on the cloud.We describe here the initiatives in EOSC-Life to implement existing tools for reproducibility as well as to develop new tools for its enhancement. As the final goal of EOSC-Life is to make data resources available to the wider community of life scientists, although necessarily technical in several points, this document aims at a general readership, including experimental in addition to data scientists.
Published: 2022

18. Varidnaviruses in the human gut: a major expansion of the order Vinavirales

Author: Natalya Yutin, Mike Rayko, Dmitry Antipov, Pascal Mutz, Yuri I. Wolf, Mart Krupovic, Eugene V. Koonin, National Center for Biotechnology Information (NCBI), Center for Algorithmic Biotechnology [Saint Petersburg], Institute of Translational Biomedicine [Saint-Petersburg], Saint Petersburg University (SPBU)-Saint Petersburg University (SPBU), Virologie des archées - Archaeal Virology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), N.Y.: P.M.: Y.I.W. and E.V.K. are funded through the Intramural Research Program of the National Insitutes of Health of the USA (National Library of Medicine), M.K. was supported by l’Agence Nationale de la Recherche grant ANR-21-CE11-0001-01., and ANR-21-CE11-0001,ArcFus,Protéines de classe II de fusion membranaire chez les archées(2021)
Subjects: human gut metagenome, Infectious Diseases, double jelly roll capsid, Varidnaviria, Vinavirales, Corticoviridae, Autolykiviridae, Virology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology
Abstract: BackgroundBacteriophages play key roles in the dynamics of the human microbiome. By far the most abundant components of the human gut virome are tailed bacteriophages of the realm Duplodnaviria, in particular, crAss-like phages. However, apart from duplodnaviruses, the gut virome has not been dissected in detail.ResultsHere we report a comprehensive census of a minor component of the gut virome, the tailless bacteriophages of the realm Varidnaviria. Tailless phages are primarily represented in the gut by prophages of the families Corticoviridae and Autolykiviridae that jointly comprise the order Vinavirales and are mostly integrated as prophages in genomes of Alphaproteobacteria and Verrucomicrobia. Phylogenetic analysis of the major capsid proteins (MCP) and packaging ATPases suggests that at least three new families within Vinavirales should be established to accommodate the diversity of prophages from the human gut virome. Previously, only the MCP and ATPase genes were reported to be conserved in all members of Vinavirales. Here we identify a core set of 12 proteins that are shared by most of these viruses including previously undetected lysis enzymes. We further demonstrate that replication system components are frequently replaced in the genomes of Vinavirales, suggestive of selective pressure for escape from yet unknown host defenses or avoidance of incompatibility with coinfecting related viruses.ConclusionsThe results of this analysis show that, in a sharp contrast to marine viromes, varidnaviruses are a minor component of the human gut virome. Moreover, they are primarily represented by proviruses, suggesting that there are few if any active varidnavirus infections in the gut at any given time. These findings complement the existing knowledge of the human gut virome by exploring a group of viruses that was virtually overlooked in previous work.
Published: 2022

19. The logic of virus evolution

Author: Eugene V. Koonin, Valerian V. Dolja, Mart Krupovic, National Center for Biotechnology Information (NCBI), Oregon State University (OSU), Virologie des archées - Archaeal Virology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), E.V.K. is supported by the Intramural Research Program of the National Institutes of Health of the USA (National Library of Medicine). M.K. was supported by l’Agence Nationale de la Recherche grant ANR-21-CE11-0001-01. V.V.D. was partially supported by an NIH/NLM/NCBI Visiting Scientist Fellowship., and ANR-21-CE11-0001,ArcFus,Protéines de classe II de fusion membranaire chez les archées(2021)
Subjects: virus evolution, Genes, Viral, Logic, Microbiology, Biological Evolution, origins of viruses, Evolution, Molecular, Virology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Viruses, exaptation, Parasitology, Capsid Proteins, virus structure, Virus Physiological Phenomena
Abstract: International audience; Viruses are obligate intracellular parasites. Despite their dependence on host cells, viruses are evolutionarily autonomous, with their own genomes and evolutionary trajectories locked in arms races with the hosts. Here, we discuss a simple functional logic to explain virus macroevolution that appears to define the course of virus evolution. A small core of virus hallmark genes that are responsible for genome replication apparently descended from primordial replicators, whereas most virus genes, starting with those encoding capsid proteins, were subsequently acquired from hosts. The oldest of these acquisitions antedate the last universal cellular ancestor (LUCA). Host gene capture followed two major routes: convergent recruitment of genes with functions that directly benefit virus reproduction and exaptation when host proteins are repurposed for unique virus functions. These forms of host protein recruitment by viruses result in different levels of similarity between virus and host homologs, with the exapted ones often changing beyond easy recognition.
Published: 2022

20. Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs

Author: Benjamin D. Lee, Uri Neri, Simon Roux, Yuri I. Wolf, Antonio Pedro Camargo, Mart Krupovic, Peter Simmonds, Nikos Kyrpides, Uri Gophna, Valerian V. Dolja, Eugene V. Koonin, National Center for Biotechnology Information (NCBI), University of Oxford, Tel Aviv University (TAU), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Virologie des archées - Archaeal Virology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Oregon State University (OSU), B.D.L. was supported by a fellowship from the National Institutes of Health Oxford-Cambridge Scholars Program. Y.I.W. and E.V.K. are supported through the Intramural Research Program of the US National Institutes of Health (National Library of Medicine). U.G. and U.N. are supported by the European Research Council (ERC-AdG 787514). U.N. is partially supported by a fellowship from the Edmond J. Safra Center for Bioinformatics at Tel Aviv University. V.V.D. was partially supported by NIH/NLM/NCBI Visiting Scientist Fellowship. The work of the US Department of Energy Joint Genome Institute (S.R., N.K., and all JGI co-authors), a DOE Office of Science User Facility, is supported by the Office of Science of the US Department of Energy under contract no. DE-AC02-05CH11231. M.K. was supported by l’Agence Nationale de la Recherche grants ANR-20-CE20-009-02 and ANR-21-CE11-0001-01., ANR-20-CE20-0009,VIROMET,Devoiler le virome des archées methanogenes(2020), and ANR-21-CE11-0001,ArcFus,Protéines de classe II de fusion membranaire chez les archées(2021)
Subjects: [SDV]Life Sciences [q-bio], General Biochemistry, Genetics and Molecular Biology
Abstract: International audience; Viroids and viroid-like covalently closed circular (ccc) RNAs are minimal replicators that typically encode no proteins and hijack cellular enzymes for replication. The extent and diversity of viroid-like agents are poorly understood. We developed a computational pipeline to identify viroid-like cccRNAs and applied it to 5,131 metatranscriptomes and 1,344 plant transcriptomes. The search yielded 11,378 viroid-like cccRNAs spanning 4,409 species-level clusters, a 5-fold increase compared to the previously identified viroid-like elements. Within this diverse collection, we discovered numerous putative viroids, satellite RNAs, retrozymes, and ribozy-like viruses. Diverse ribozyme combinations and unusual ribozymes within the cccRNAs were identified. Self-cleaving ribozymes were identified in ambiviruses, some mito-like viruses and capsid-encoding satellite virus-like cccRNAs. The broad presence of viroid-like cccRNAs in diverse transcriptomes and ecosystems implies that their host range is far broader than currently known, and matches to CRISPR spacers suggest that some cccRNAs replicate in prokaryotes.
Published: 2023

21. Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations

Author: Qingyu Chen, Alexis Allot, Robert Leaman, Rezarta Islamaj, Jingcheng Du, Li Fang, Kai Wang, Shuo Xu, Yuefu Zhang, Parsa Bagherzadeh, Sabine Bergler, Aakash Bhatnagar, Nidhir Bhavsar, Yung-Chun Chang, Sheng-Jie Lin, Wentai Tang, Hongtong Zhang, Ilija Tavchioski, Senja Pollak, Shubo Tian, Jinfeng Zhang, Yulia Otmakhova, Antonio Jimeno Yepes, Hang Dong, Honghan Wu, Richard Dufour, Yanis Labrak, Niladri Chatterjee, Kushagri Tandon, Fréjus A A Laleye, Loïc Rakotoson, Emmanuele Chersoni, Jinghang Gu, Annemarie Friedrich, Subhash Chandra Pujari, Mariia Chizhikova, Naveen Sivadasan, Saipradeep VG, Zhiyong Lu, National Center for Biotechnology Information (NCBI), Traitement Automatique du Langage Naturel (LS2N - équipe TALN ), Laboratoire des Sciences du Numérique de Nantes (LS2N), Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-École Centrale de Nantes (Nantes Univ - ECN), Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes université - UFR des Sciences et des Techniques (Nantes univ - UFR ST), Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Nantes Université (Nantes Univ), Laboratoire Informatique d'Avignon (LIA), Avignon Université (AU)-Centre d'Enseignement et de Recherche en Informatique - CERI, Université d'Avignon, and Zenidoc
Subjects: FOS: Computer and information sciences, Computer Science - Machine Learning, PubMed, Databases, Factual, Data Mining/methods, General Biochemistry, Genetics and Molecular Biology, Machine Learning (cs.LG), Computer Science - Information Retrieval, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], Data Mining, Humans, Digital Libraries (cs.DL), [INFO]Computer Science [cs], COVID-19/epidemiology, Computer Science - Computation and Language, Publications, COVID-19, Computer Science - Digital Libraries, [INFO.INFO-TT]Computer Science [cs]/Document and Text Processing, Original Article, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], ddc:004, General Agricultural and Biological Sciences, Computation and Language (cs.CL), Information Retrieval (cs.IR), Information Systems
Abstract: The coronavirus disease 2019 (COVID-19) pandemic has been severely impacting global society since December 2019. The related findings such as vaccine and drug development have been reported in biomedical literature—at a rate of about 10 000 articles on COVID-19 per month. Such rapid growth significantly challenges manual curation and interpretation. For instance, LitCovid is a literature database of COVID-19-related articles in PubMed, which has accumulated more than 200 000 articles with millions of accesses each month by users worldwide. One primary curation task is to assign up to eight topics (e.g. Diagnosis and Treatment) to the articles in LitCovid. The annotated topics have been widely used for navigating the COVID literature, rapidly locating articles of interest and other downstream studies. However, annotating the topics has been the bottleneck of manual curation. Despite the continuing advances in biomedical text-mining methods, few have been dedicated to topic annotations in COVID-19 literature. To close the gap, we organized the BioCreative LitCovid track to call for a community effort to tackle automated topic annotation for COVID-19 literature. The BioCreative LitCovid dataset—consisting of over 30 000 articles with manually reviewed topics—was created for training and testing. It is one of the largest multi-label classification datasets in biomedical scientific literature. Nineteen teams worldwide participated and made 80 submissions in total. Most teams used hybrid systems based on transformers. The highest performing submissions achieved 0.8875, 0.9181 and 0.9394 for macro-F1-score, micro-F1-score and instance-based F1-score, respectively. Notably, these scores are substantially higher (e.g. 12%, higher for macro F1-score) than the corresponding scores of the state-of-art multi-label classification method. The level of participation and results demonstrate a successful track and help close the gap between dataset curation and method development. The dataset is publicly available via https://ftp.ncbi.nlm.nih.gov/pub/lu/LitCovid/biocreative/ for benchmarking and further development. Database URL https://ftp.ncbi.nlm.nih.gov/pub/lu/LitCovid/biocreative/
Published: 2022

22. Deep Roots and Splendid Boughs of the Global Plant Virome

Author: Valerian V. Dolja, Mart Krupovic, Eugene V. Koonin, Department of Botany and Plant Pathology, Oregon State University (OSU), Center for Genome Research and Biocomputing, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris], National Library of Medicine (NLM), National Institutes of Health [Bethesda] (NIH)-National Center for Biotechnology Information (NCBI), and Institut Pasteur [Paris] (IP)
Subjects: 0301 basic medicine, 030106 microbiology, Plant Science, Biology, virus taxonomy, phylogeny, Plant Viruses, 03 medical and health sciences, plant virus, Phylogenetics, Plant virus, RNA Viruses, Human virome, Coevolution, Virus classification, virus evolution, virome, fungi, food and beverages, Plants, 030104 developmental biology, Evolutionary biology, Viral evolution, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Taxonomy (biology), Mobile genetic elements
Abstract: International audience; Land plants host a vast and diverse virome that is dominated by RNA viruses, with major additional contributions from reverse-transcribing and single-stranded (ss) DNA viruses. Here, we introduce the recently adopted comprehensive taxonomy of viruses based on phylogenomic analyses, as applied to the plant virome. We further trace the evolutionary ancestry of distinct plant virus lineages to primordial genetic mobile elements. We discuss the growing evidence of the pivotal role of horizontal virus transfer from invertebrates to plants during the terrestrialization of these organisms, which was enabled by the evolution of close ecological associations between these diverse organisms. It is our hope that the emerging big picture of the formation and global architecture of the plant virome will be of broad interest to plant biologists and virologists alike and will stimulate ever deeper inquiry into the fascinating field of virus-plant coevolution.
Published: 2020

23. The LUCA and its complex virome

Author: Mart Krupovic, Valerian V. Dolja, Eugene V. Koonin, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris], Department of Botany and Plant Pathology, Oregon State University (OSU), National Library of Medicine (NLM), National Institutes of Health [Bethesda] (NIH)-National Center for Biotechnology Information (NCBI), E.V.K. is supported by the funds of the Intramural Research Program of the National Institutes of Health of the USA. M.K. was supported by l’Agence Nationale de la Recherche grant ANR-17-CE15-0005-01., ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), and Institut Pasteur [Paris] (IP)
Subjects: Evolution, [SDV]Life Sciences [q-bio], Population, Genome, Viral, Biology, Microbiology, Genome, Evolution, Molecular, Viral Proteins, 03 medical and health sciences, Virology, Three-domain system, Human virome, education, Gene, Ancestor, 0303 health sciences, education.field_of_study, Bacteria, General Immunology and Microbiology, Virome, 030306 microbiology, Archaea, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Infectious Diseases, Evolutionary biology, Viral evolution, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Capsid Proteins, Mobile genetic elements
Abstract: The last universal cellular ancestor (LUCA) is the most recent population of organisms from which all cellular life on Earth descends. The reconstruction of the genome and phenotype of the LUCA is a major challenge in evolutionary biology. Given that all life forms are associated with viruses and/or other mobile genetic elements, there is no doubt that the LUCA was a host to viruses. Here, by projecting back in time using the extant distribution of viruses across the two primary domains of life, bacteria and archaea, and tracing the evolutionary histories of some key virus genes, we attempt a reconstruction of the LUCA virome. Even a conservative version of this reconstruction suggests a remarkably complex virome that already included the main groups of extant viruses of bacteria and archaea. We further present evidence of extensive virus evolution antedating the LUCA. The presence of a highly complex virome implies the substantial genomic and pan-genomic complexity of the LUCA itself. The last universal cellular ancestor (LUCA) is the most recent population of organisms from which all cellular life on Earth descends. In this Perspective article, Krupovic, Dolja and Koonin analyse the extant distribution of viruses across the two primary domains of life to infer the LUCA virome.
Published: 2020

24. Machine Learning Neuroprotective Strategy Reveals a Unique Set of Parkinson Therapeutic Nicotine Analogs

Author: Rojas-Rodríguez, Felipe, Morantes, Carlos, Pinzón, Andrés, Barreto, George E., Cabezas, Ricardo, Mariño-Ramírez, Leonardo, González, Janneth, Intramural Research Program of the National Institutes of Health (USA), National Library of Medicine (USA), and National Center for Biotechnology Information (NCBI)
Subjects: substanita nigra, PI3K/AKT, machine learning, Substanita Nigra, Machine learning, Parkinson’s disease, Nicotine analogs, nicotine analogs, artificial neural networks, Article, Artificial Neural Networks
Abstract: Aims: Present a novel machine learning computational strategy to predict the neuroprotection potential of nicotine analogs acting over the behavior of unpaired signaling pathways in Parkinson’s disease. Background: Dopaminergic replacement has been used for Parkinson’s Disease (PD) treatment with positive effects on motor symptomatology but low progression and prevention effects. Epidemiological studies have shown that nicotine consumption decreases PD prevalence through neuroprotective mechanisms activation associated with the overstimulation of signaling pathways (SP) such as PI3K/AKT through nicotinic acetylcholine receptors (e.g α7 nAChRs) and over-expression of anti-apoptotic genes such as Bcl-2. Nicotine analogs with similar neuroprotective activity but decreased secondary effects remain as a promissory field. Objective: The objective of this study is to develop an interdisciplinary computational strategy predicting the neuroprotective activity of a series of 8 novel nicotine analogs over Parkinson’s disease. Methods: We present a computational strategy integrating structural bioinformatics, SP manual reconstruction, and deep learning to predict the potential neuroprotective activity of 8 novel nicotine analogs over the behavior of PI3K/AKT. We performed a protein-ligand analysis between nicotine analogs and α7 nAChRs receptor using geometrical conformers, physicochemical characterization of the analogs and developed manually curated neuroprotective datasets to analyze their potential activity. Additionally, we developed a predictive machine-learning model for neuroprotection in PD through the integration of Markov Chain Monte-Carlo transition matrix for the 2 SP with synthetic training datasets of the physicochemical properties and structural dataset. Results: Our model was able to predict the potential neuroprotective activity of seven new nicotine analogs based on the binomial Bcl-2 response regulated by the activation of PI3K/AKT. Conclusion: Hereby, we present a robust novel strategy to assess the neuroprotective potential of biomolecules based on SP architecture. Our theoretical strategy can be further applied to the study of new treatments related to SP deregulation and may ultimately offer new opportunities for therapeutic interventions in neurodegenerative diseases.
Published: 2020

25. Multilateral benefit-sharing from digital sequence information will support both science and biodiversity conservation

Author: Amber Hartman Scholz, Jens Freitag, Christopher H. C. Lyal, Rodrigo Sara, Martha Lucia Cepeda, Ibon Cancio, Scarlett Sett, Andrew Lee Hufton, Yemisrach Abebaw, Kailash Bansal, Halima Benbouza, Hamadi Iddi Boga, Sylvain Brisse, Michael W. Bruford, Hayley Clissold, Guy Cochrane, Jonathan A. Coddington, Anne-Caroline Deletoille, Felipe García-Cardona, Michelle Hamer, Raquel Hurtado-Ortiz, Douglas W. Miano, David Nicholson, Guilherme Oliveira, Carlos Ospina Bravo, Fabian Rohden, Ole Seberg, Gernot Segelbacher, Yogesh Shouche, Alejandra Sierra, Ilene Karsch-Mizrachi, Jessica da Silva, Desiree M. Hautea, Manuela da Silva, Mutsuaki Suzuki, Kassahun Tesfaye, Christian Keambou Tiambo, Krystal A. Tolley, Rajeev Varshney, María Mercedes Zambrano, Jörg Overmann, European Commission, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), The Natural History Museum [London] (NHM), One Planet Solutions, Montpellier, Universidad de los Andes [Bogota] (UNIANDES), European Marine Biological Resource Centre (EMBRC-ERIC), Ethiopian Biotechnology Institute, Addis Ababa, National Academy of Agricultural Science and Global Plant Council, New Delhi, National Council of Scientific Research and Technologies (NCSRT), Algiers (NCSRT), Ministry of Agriculture, Livestock, Fisheries and Cooperatives, Nairobi, Institut Pasteur [Paris] (IP), Cardiff University, The Wellcome Trust Sanger Institute [Cambridge], European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Global Genome Initiative, Smithsonian National Museum of Natural History, Washington, DC, Alexander von Humboldt Biological Resources Research Institute, Bogota, South African National Biodiversity Institute, University of Nairobi (UoN), Instituto Tecnológico Vale [Belém, Brazil] (ITV), Ministry of the Environment and Sustainable Developmentment, University of Lethbridge, Natural History Museum of Denmark, Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), University of Freiburg [Freiburg], National Centre for Cell Science [Pune, India] (NCCS), Mariano Galvez University, Guatemala City, National Center for Biotechnology Information (NCBI), University of Johannesburg [South Africa] (UJ), University of the Philippines Los Baños (UP Los Baños), Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP), National Institute of Genetics (NIG), Institute of Biotechnology [Vilnius], Life Science Center [Vilnius], Vilnius University [Vilnius]-Vilnius University [Vilnius], Centre for Tropical Livestock Genetics and Health [Edimburgh] (CTLGH), Murdoch University, Corporación CorpoGen, Bogota, Technische Universität Braunschweig = Technical University of Braunschweig [Braunschweig], This work was funded by the German Federal Ministry of Education and Research (BMBF) WiLDSI 031B0862 (A.H.S., J.O., and J.F.) and Horizon Europe EVA-GLOBAL 871029 (A.H.S.). I.K.M. was supported by the National Center for Biotechnology Information of the National Library of Medicine, National Institutes of Health., European Project: 871029,H2020,H2020-INFRAIA-2019-1,EVA-GLOBAL(2020), and European Project: 01UU1602A/C
Subjects: Conservation of Natural Resources, Multidisciplinary, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, General Physics and Astronomy, General Chemistry, Biodiversity, General Biochemistry, Genetics and Molecular Biology
Abstract: Open access to sequence data is a cornerstone of biology and biodiversity research, but has created tension under the United Nations Convention on Biological Diversity (CBD). Policy decisions could compromise research and development, unless a practical multilateral solution is implemented. This workwas funded by the German Federal Ministry of Education and Research (BMBF) WiLDSI 031B0862 (A.H.S., J.O., and J.F.) and Horizon Europe EVA-GLOBAL 871029 (A.H.S.). I.K.M. was supported by the National Center for Biotechnology Information of the National Library of Medicine, National Institutes of Health.
Published: 2022
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26. Viruses Defined by the Position of the Virosphere within the Replicator Space

Author: Mart Krupovic, Valerian V. Dolja, Jens H. Kuhn, Eugene V. Koonin, National Center for Biotechnology Information (NCBI), Oregon State University (OSU), Virologie des archées - Archaeal Virology, Institut Pasteur [Paris] (IP), Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), V.K. is supported by the Intramural Research Program of the National Institutes of Health of the USA (National Library of Medicine). This work was supported in part through Laulima Government Solutions, LLC, prime contract with the U.S. National Institute of Allergy and Infectious Diseases (NIAID) under contract no. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC, under contract no. HHSN272201800013C. M.K. was supported by l’Agence Nationale de la Recherche (grant ANR-20-CE20-0009) and Emergence(s) project MEMREMA from Ville de Paris., and ANR-20-CE20-0009,VIROMET,Devoiler le virome des archées methanogenes(2020)
Subjects: viruses, Virtual space, replicator, virus, Review, Biology, Space (commercial competition), virus taxonomy, Microbiology, Genome, Defective virus, 03 medical and health sciences, virus classification, Molecular Biology, Virus classification, Host protein, virosphere, 030304 developmental biology, perivirosphere, 0303 health sciences, orthovirosphere, 030306 microbiology, mobile genetic element, MGE, DNA Viruses, DNA, Biological Evolution, Infectious Diseases, Evolutionary biology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Viruses, virus definition, Plasmids
Abstract: International audience; Originally, viruses were defined as miniscule infectious agents that passed through filters that retain even the smallest cells. Subsequently, viruses were considered obligate intracellular parasites whose reproduction depends on their cellular hosts for energy supply and molecular building blocks. However, these features are insufficient to unambiguously define viruses as they are broadly understood today. We outline possible approaches to define viruses and explore the boundaries of the virosphere within the virtual space of replicators and the relationships between viruses and other types of replicators. Regardless of how, exactly, viruses are defined, viruses clearly have evolved on many occasions from nonviral replicators, such as plasmids, by recruiting host proteins to become virion components. Conversely, other types of replicators have repeatedly evolved from viruses. Thus, the virosphere is a dynamic entity with extensive evolutionary traffic across its boundaries. We argue that the virosphere proper, here termed orthovirosphere, consists of a distinct variety of replicators that encode structural proteins encasing the replicators' genomes, thereby providing protection and facilitating transmission among hosts. Numerous and diverse replicators, such as virus-derived but capsidless RNA and DNA elements, or defective viruses occupy the zone surrounding the orthovirosphere in the virtual replicator space. We define this zone as the perivirosphere. Although intense debates on the nature of certain replicators that adorn the internal and external boundaries of the virosphere will likely continue, we present an operational definition of virus that recently has been accepted by the International Committee on Taxonomy of Viruses.
Published: 2021

27. Perspective on taxonomic classification of uncultivated viruses

Author: Dutilh, Bas E, Varsani, Arvind, Tong, Yigang, Simmonds, Peter, Sabanadzovic, Sead, Rubino, Luisa, Roux, Simon, Muñoz, Alejandro Reyes, Lood, Cédric, Lefkowitz, Elliot J, Kuhn, Jens H, Krupovic, Mart, Edwards, Robert A, Brister, J Rodney, Adriaenssens, Evelien M, Sullivan, Matthew B, Theoretical Biology and Bioinformatics, Sub Bioinformatics, Utrecht University [Utrecht], Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], Arizona State University [Tempe] (ASU), University of Cape Town, Beijing University of Chemical Technology, University of Oxford [Oxford], Mississippi State University [Mississippi], Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] (IPSP), Consiglio Nazionale delle Ricerche (CNR), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Universidad de los Andes [Bogota] (UNIANDES), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), University of Alabama at Birmingham [ Birmingham] (UAB), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Virologie des archées - Archaeal Virology, Institut Pasteur [Paris], Flinders University [Adelaide, Australia], National Library of Medicine (NLM), National Institutes of Health [Bethesda] (NIH)-National Center for Biotechnology Information (NCBI), Quadram Institute Bioscience (QIB), Ohio State University [Columbus] (OSU), BED is supported by the European Research Council (ERC) Consolidator grant 865694: DiversiPHI. CL is supported by the Research Foundation Flanders (FWO) SB grant 1S64720N. RAE is supported by the National Institute of Diabetes and Digestive and Kidney Diseases of the National Institutes of Health (NIH) under Award Number RC2DK116713. SR is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. This work was also supported in part through Laulima Government Solutions, LLC, prime contract with the NIH National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272201800013C. JHK performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC, under Contract No. HHSN272201800013C. SS acknowledges partial support from the Special Research Initiative (MAFES), Mississippi State University, and the National Institute of Food and Agriculture, U.S. Department of Agriculture, Hatch Project 1021494. EMA acknowledges the support of the Biotechnology and Biological Sciences Research Council (BBSRC), this research was funded by the BBSRC Institute Strategic Programme Gut Microbes and HealthBB/R012490/1 and its constituent projects BBS/E/F/000PR10353 and BBS/E/F/000PR10356. This research was supported in part by the Intramural Research Program of the National Library of Medicine at the NIH, National Library of Medicine. MBS was supported by the U.S. National Science Foundation award ABI#1759874., European Project: 865694,H2020-EU.1.1. - EXCELLENT SCIENCE - European Research Council (ERC),DiversiPHI(2020), University of Oxford, CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] (IPSP), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Quadram Institute Bioscience [Norwich, U.K.] (QIB), Biotechnology and Biological Sciences Research Council (BBSRC), Theoretical Biology and Bioinformatics, and Sub Bioinformatics
Subjects: BACTERIAL, Evolution, viruses, Biology, Microbiology, SEQUENCE, Evolution, Molecular, 03 medical and health sciences, ICTV, Data sequences, Virology, Animals, Humans, 10. No inequality, PROGRESS, Phylogeny, Virus classification, 030304 developmental biology, 0303 health sciences, Science & Technology, 030306 microbiology, Molecular, Biological classification, EXPANSION, Taxon, Medical Microbiology, Metagenomics, Evolutionary biology, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, ICTV BACTERIAL, UPDATE, Life Sciences & Biomedicine
Abstract: Historically, virus taxonomy has been limited to describing viruses that were readily cultivated in the laboratory or emerging in natural biomes. Metagenomic analyses, single-particle sequencing, and database mining efforts have yielded new sequence data on an astounding number of previously unknown viruses. As metagenomes are relatively free of biases, these data provide an unprecedented insight into the vastness of the virosphere, but to properly value the extent of this diversity it is critical that the viruses are taxonomically classified. Inclusion of uncultivated viruses has already improved the process as well as the understanding of the taxa, viruses, and their evolutionary relationships. The continuous development and testing of computational tools will be required to maintain a dynamic virus taxonomy that can accommodate the new discoveries. ispartof: CURRENT OPINION IN VIROLOGY vol:51 pages:1-9 ispartof: location:Netherlands status: published
Published: 2021

28. In vivo commensal control of Clostridioides difficile virulence

Author: Mario L. Arrieta-Ortiz, Johann Peltier, Andrew B. Onderdonk, Selva Rupa Christinal Immanuel, Narjol Gonzalez-Escalona, Nicholas DiBenedetto, Richard Lavin, Nitin S. Baliga, Marc W. Allard, Maria Hoffman, Abraham L. Sonenshein, Yan Luo, Christopher K Cummins, Brintha P. Girinathan, Lynn Bry, Bruno Dupuy, Jay N. Worley, Mary L. Delaney, Georg K. Gerber, Brigham & Women’s Hospital [Boston] (BWH), Harvard Medical School [Boston] (HMS), National Center for Biotechnology Information (NCBI), Pathogénèse des Bactéries Anaérobies / Pathogenesis of Bacterial Anaerobes (PBA (U-Pasteur_6)), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institute for Systems Biology [Seattle] (ISB), U.S. Food and Drug Administration (FDA), Harvard-MIT Division of Health Sciences and Technology [Cambridge], Massachusetts Institute of Technology (MIT), Tufts University School of Medicine [Boston], This work was supported by the BWH Precision Medicine Institute, R01AI153605 from the National Institute of Allergy and Infectious Diseases (NIAID) and P30DK034854 from the National Institute of Diabetes, Digestive and Kidney Diseases to L.B., R01AI128215, R01AI141953, and U19AI135976 from NIAID and IIBR-2042948 from the National Science Foundation to N.S.B., B.P.G. was supported by T32 HL007627, and the work of J.N.W. was supported by the Intramural Research Program of the National Library of Medicine, National Institutes of Health. J.P. received support from the Institut Pasteur (Bourse ROUX). This work was conducted by authors from the FDA working as official U.S. Government employees and for which no additional external funding was utilized.
Subjects: MESH: Clostridioides difficile, MESH: Amino Acids, colitis, Systems biology, MESH: Clostridium Infections, [SDV]Life Sciences [q-bio], gnotobiotic mouse, Clostridium sardiniense, Virulence, MESH: Butyrates, Biology, MESH: Virulence, medicine.disease_cause, Microbiology, MESH: Clostridiales, MESH: Fermentation, Clostridia, MESH: Gene Expression Profiling, conventional mouse, In vivo, Virology, MESH: Germ-Free Life, MESH: Severity of Illness Index, medicine, Paraclostridium bifermentans, MESH: Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Colitis, Pathogen, MESH: Mice, MESH: Gene Regulatory Networks, MESH: Gene Expression Regulation, Bacterial, metatranscriptomics, MESH: Symbiosis, Toxin, Host (biology), Clostridioides difficile, MESH: Clostridium, MESH: Arginine, MESH: Cecum, biology.organism_classification, medicine.disease, metabolomics, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, MESH: Systems Biology, Parasitology, carbon source enrichment analysis, anaerobe metabolism
Abstract: International audience; Leveraging systems biology approaches, we illustrate how metabolically distinct species of Clostridia protect against or worsen Clostridioides difficile infection in mice by modulating the pathogen's colonization, growth, and virulence to impact host survival. Gnotobiotic mice colonized with the amino acid fermenter Paraclostridium bifermentans survive infection with reduced disease severity, while mice colonized with the butyrate-producer, Clostridium sardiniense, succumb more rapidly. Systematic in vivo analyses revealed how each commensal alters the gut-nutrient environment to modulate the pathogen's metabolism, gene regulatory networks, and toxin production. Oral administration of P. bifermentans rescues conventional, clindamycin-treated mice from lethal C. difficile infection in a manner similar to that of monocolonized animals, thereby supporting the therapeutic potential of this commensal species. Our findings lay the foundation for mechanistically informed therapies to counter C. difficile disease using systems biology approaches to define host-commensal-pathogen interactions in vivo.
Published: 2021

29. The Baltimore Classification of Viruses 50 Years Later: How Does It Stand in the Light of Virus Evolution?

Author: Vadim I. Agol, Eugene V. Koonin, Mart Krupovic, National Center for Biotechnology Information (NCBI), Virologie des archées - Archaeal Virology, Institut Pasteur [Paris] (IP), Russian Academy of Sciences [Moscow] (RAS), Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University (MSU), E.V.K. was supported by the Intramural Research Program of the National Institutes of Health of the USA (National Library of Medicine). M.K. was supported by l’Agence Nationale de la Recherche (grant ANR-20-CE20-0009) and Emergence(s) project MEMREMA from Ville de Paris. V.I.A. was supported by the Russian Science Foundation grant number 20-14-00178., and ANR-20-CE20-0009,VIROMET,Devoiler le virome des archées methanogenes(2020)
Subjects: Genes, Viral, Ecology (disciplines), Review, Genome, Viral, Biology, virus taxonomy, Microbiology, Genome, Virus, Evolution, Molecular, 03 medical and health sciences, Monophyly, Baltimore classification, Conceptual foundation, Animals, Humans, virus classification, Molecular Biology, Virus classification, Phylogeny, 030304 developmental biology, virus evolution, virus realms, 0303 health sciences, 030306 microbiology, DNA, Infectious Diseases, Evolutionary biology, Viral evolution, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Viruses
Abstract: International audience; Fifty years ago, David Baltimore published a brief conceptual paper delineating the classification of viruses by the routes of genome expression. The six "Baltimore classes" of viruses, with a subsequently added 7th class, became the conceptual framework for the development of virology during the next five decades. During this time, it became clear that the Baltimore classes, with relatively minor additions, indeed cover the diversity of virus genome expression schemes that also define the replication cycles. Here, we examine the status of the Baltimore classes 50 years after their advent and explore their links with the global ecology and biology of the respective viruses. We discuss an extension of the Baltimore scheme and why many logically admissible expression-replication schemes do not appear to be realized in nature. Recent phylogenomic analyses allow tracing the complex connections between the Baltimore classes and the monophyletic realms of viruses. The five classes of RNA viruses and reverse-transcribing viruses share an origin, whereas both the single-stranded DNA viruses and double-stranded DNA (dsDNA) viruses evolved on multiple independent occasions. Most of the Baltimore classes of viruses probably emerged during the earliest era of life evolution, at the stage of the primordial pool of diverse replicators, and before the advent of modern-like cells with large dsDNA genomes. The Baltimore classes remain an integral part of the conceptual foundation of biology, providing the essential structure for the logical space of information transfer processes, which is nontrivially connected with the routes of evolution of viruses and other replicators.
Published: 2021

30. Author Correction: Improved reference genome of the arboviral vector Aedes albopictus

Author: Pascal Miesen, Rebecca Halbach, Omar S. Akbari, Philippos Aris Papathanos, Elisa Pischedda, Ronald P. van Rij, Flavia Krsticevic, Françoise Thibaud-Nissen, Atashi Sharma, Arang Rhie, Luciano V. Cosme, Michele Marconcini, Zhijian Tu, Anna-Bella Failloux, Jeffrey R. Powell, Maria V. Sharakhova, James K. Biedler, Jacob E. Crawford, Reem A. Masri, Sergey Koren, D. A. Karagodin, Igor Antoshechkin, Jeremy Jenrette, Stephanie Gamez, Adam M. Phillippy, Umberto Palatini, Adalgisa Caccone, Mariangela Bonizzoni, J. Spencer Johnston, Patrick Masterson, Jay Ghurye, Università degli Studi di Pavia, Virginia Polytechnic Institute and State University [Blacksburg], Yale University [New Haven], National Human Genome Research Institute (NHGRI), National Center for Biotechnology Information (NCBI), The Hebrew University of Jerusalem (HUJ), Texas A&M University [College Station], Radboud Institute for Molecular Life Sciences [Nijmegen, the Netherlands], Verily Life Sciences Inc, California Institute of Technology (CALTECH), Arbovirus et Insectes Vecteurs - Arboviruses and Insect Vectors, Institut Pasteur [Paris], Siberian Branch of the Russian Academy of Sciences (SB RAS), University of California [San Diego] (UC San Diego), University of California, Tomsk State University [Tomsk], Università degli Studi di Pavia = University of Pavia (UNIPV), Institut Pasteur [Paris] (IP), and University of California (UC)
Subjects: Aedes albopictus, QH301-705.5, [SDV]Life Sciences [q-bio], Computational biology, Mosquito Vectors, Biology, QH426-470, Chromosomes, 03 medical and health sciences, 0302 clinical medicine, Genome Size, Aedes, Genetics, Animals, RNA, Small Interfering, Biology (General), Author Correction, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Genome, Immunity, Chromosome Mapping, biology.organism_classification, Human genetics, 3. Good health, Insect Vectors, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Vector (epidemiology), [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Transcriptome, 030217 neurology & neurosurgery, Arboviruses, Reference genome
Abstract: The Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary approach to prevent mosquito-borne diseases. A reliable and accurate DNA sequence of the Ae. albopictus genome is essential to develop new approaches that involve genetic manipulation of mosquitoes.We use long-read sequencing methods and modern scaffolding techniques (PacBio, 10X, and Hi-C) to produce AalbF2, a dramatically improved assembly of the Ae. albopictus genome. AalbF2 reveals widespread viral insertions, novel microRNAs and piRNA clusters, the sex-determining locus, and new immunity genes, and enables genome-wide studies of geographically diverse Ae. albopictus populations and analyses of the developmental and stage-dependent network of expression data. Additionally, we build the first physical map for this species with 75% of the assembled genome anchored to the chromosomes.The AalbF2 genome assembly represents the most up-to-date collective knowledge of the Ae. albopictus genome. These resources represent a foundation to improve understanding of the adaptation potential and the epidemiological relevance of this species and foster the development of innovative control measures.
Published: 2021

31. Minimum Information about an Uncultivated Virus Genome (MIUViG)

Author: Seth R. Bordenstein, Frederik Schulz, Pelin Yilmaz, Rebecca Vega Thurber, Natalia Ivanova, Christelle Desnues, Shinichi Sunagawa, Karyna Rosario, Simon Roux, Steven W. Wilhelm, Nicole S. Webster, Mart Krupovic, Lisa Zeigler Allen, Catherine Putonti, K. Eric Wommack, Tanja Woyke, Eugene V. Koonin, Joanne B. Emerson, Jed A. Fuhrman, Hiroyuki Ogata, Ramy K. Aziz, Arvind Varsani, Marie-Agnès Petit, Bonnie L. Hurwitz, Evelien M. Adriaenssens, Andrew M. Kropinski, Katrine Whiteson, Thomas Rattei, Kyung Bum Lee, Peer Bork, David Paez-Espino, Mark J. Young, Jens H. Kuhn, Ben Temperton, Rebecca A. Daly, Natalya Yutin, Emiley A. Eloe-Fadrosh, Manuel Martinez-Garcia, Curtis A. Suttle, Susannah G. Tringe, Alejandro Reyes, Bas E. Dutilh, Nikos C. Kyrpides, Rex R. Malmstrom, Ilene Karsch Mizrachi, Kelly C. Wrighton, Rob Lavigne, Mya Breitbart, Lynn M. Schriml, Philip Hugenholtz, Melissa B. Duhaime, François Enault, Pascal Hingamp, Francisco Rodriguez-Valera, Clara Amid, Matthew B. Sullivan, Jessica M. Labonté, Grieg F. Steward, J. Rodney Brister, Takashi Yoshida, Guy Cochrane, DOE Joint Genome Institute [Walnut Creek], University of Liverpool, Theoretical Biology & Bioinformatics [Utrecht], University Medical Center [Utrecht], Radboud University Medical Center [Nijmegen], National Center for Biotechnology Information (NCBI), University of Guelph, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Arizona State University [Tempe] (ASU), University of Cape Town, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Cairo University, Vanderbilt University [Nashville], European Molecular Biology Laboratory [Heidelberg] (EMBL), University of South Florida [Tampa] (USF), Colorado State University [Fort Collins] (CSU), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), University of Michigan [Ann Arbor], University of Michigan System, University of California [Davis] (UC Davis), University of California (UC), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), University of Southern California (USC), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), University of Queensland [Brisbane], University of Arizona, Texas A&M University [Galveston], National Institute of Genetics (NIG), Universidad de Alicante, Kyoto University, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, University of Chicago, Department of Microbiology and Ecosystem Science [Vienna], University of Vienna [Vienna], Universidad de los Andes [Bogota] (UNIANDES), Universidad Miguel Hernández [Elche] (UMH), University of Maryland School of Medicine, University of Maryland System, University of Hawai‘i [Mānoa] (UHM), Ohio State University [Columbus] (OSU), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), University of British Columbia (UBC), University of Exeter, Oregon State University (OSU), Australian Institute of Marine Science [Townsville] (AIMS Townsville), Australian Institute of Marine Science (AIMS), University of California [Irvine] (UC Irvine), The University of Tennessee [Knoxville], University of Delaware [Newark], Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, Montana State University (MSU), J. Craig Venter Institute, University of California [San Diego] (UC San Diego), This work was supported by the Laboratory Directed Research and Development Program of Lawrence Berkeley National Laboratory under US Department of Energy Contract No. DE-AC02-05CH11231 for S.R., the Netherlands Organization for Scientific Research (NWO) Vidi grant 864.14.004 for B.E.D., the Intramural Research Program of the National Library of Medicine, National Institutes of Health for E.V.K., I.K.M., J.R.B. and N.Y., the Virus-X project (EU Horizon 2020, No. 685778) for F.E. and M.K., Battelle Memorial Institute's prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272200700016I for J.H.K., the GOA grant 'Bacteriophage Biosystems' from KU Leuven for R.L., the European Molecular Biology Laboratory for C.A. and G.R.C., Cairo University Grant 2016-57 for R.K.A., National Science Foundation award 1456778, National Institutes of Health awards R01 AI132581 and R21 HD086833, and The Vanderbilt Microbiome Initiative award for S.R.B., National Science Foundation awards DEB-1239976 for M.B. and K.R. and DEB-1555854 for M.B., the NSF Early Career award DEB-1555854 and NSF Dimensions of Biodiversity #1342701 for K.C.W. and R.A.D., the Agence Nationale de la Recherche JCJC grant ANR-13-JSV6-0004 and Investissements d'Avenir Méditerranée Infection 10-IAHU-03 for C.D., the Gordon and Betty Moore Foundation Marine Microbiology Initiative No. 3779 and the Simons Foundation for J.A.F., the French government 'Investissements d'Avenir' program OCEANOMICS ANR-11-BTBR-0008 and European FEDER Fund 1166-39417 for P. Hingamp, Australian Research Council Laureate Fellowship FL150100038 to P. Hugenholtz the National Science Foundation award 1801367 and C-DEBI Research Grant for J.M.L., the Gordon and Betty Moore Foundation grant 5334 and Ministry of Economy and Competitivity refs. CGL2013-40564-R and SAF2013-49267-EXP for M.M.-G., the Grant-in-Aid for Scientific Research on Innovative Areas from the Ministry of Education, Culture, Science, Sports, and Technology (MEXT) of Japan No. 16H06429, 16K21723, and 16H06437 for H.O. and T.Y., National Science Foundation award DBI-1661357 to C.P., the Ministry of Economy and Competitivity ref CGL2016-76273-P (cofunded with FEDER funds) for F.R.-V., the Gordon and Betty Moore Foundation awards 3305 and 3790 and NSF Biological Oceanography OCE 1536989 for M.B.S., the ETH Zurich and Helmut Horten Foundation and the Novartis Foundation for Medical-Biological Research (17B077) for S.S., a BIOS-SCOPE award from Simons Foundation International and NERC award NE/P008534/1 to B.T., NSF Biological Oceanography Grant 1635913 for R.V.T., the Australian Research Council Future Fellowship FT120100480 for N.S.W., a Gilead Sciences Cystic Fibrosis Research Scholarship for K.L.W., Gordon and Better Moore Foundation Grant 4971 for S.W.W., the NSF EPSCoR grant 1736030 for K.E.W., the National Science Foundation award DEB-4W4596 and National Institutes of Health award R01 GM117361 for M.J.Y., the Gordon and Betty Moore Foundation No. 7000 and the National Oceanic and Atmospheric Administration (NOAA) under award NA15OAR4320071 for L.Z.A. DDBJ is supported by ROIS and MEXT. The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under contract no. DE-AC02-05CH11231. The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the US Department of Health and Human Services or of the institutions and companies affiliated with the authors. B.E.D., A.K., M.K., J.H.K., R.L. and A.V. are members of the ICTV Executive Committee, but the views and opinions expressed are those of the authors and not those of the ICTV., Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Ecología Microbiana Molecular, Institut Pasteur [Paris], University of South Florida (USF), University of California, Laboratoire Microorganismes : Génome et Environnement - Clermont Auvergne (LMGE), Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Kyoto University [Kyoto], Universidad de los Andes [Bogota], Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), University of California [Irvine] (UCI), J Craig Venter Institute, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Sub Bioinformatics, and Theoretical Biology and Bioinformatics
Subjects: [SDV]Life Sciences [q-bio], Microbiología, 2.2 Factors relating to physical environment, Applied Microbiology and Biotechnology, Genome, 0302 clinical medicine, Databases, Genetic, Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14], phage, Viral, 0303 health sciences, Genetic Databases, Environmental microbiology, pipeline, Genome project, dynamics, Genomics, annotation, Viruses, Molecular Medicine, tacomony, Infection, Genetic databases, Biotechnology, Virus Cultivation, In silico, Biomedical Engineering, Phage biology, Bioengineering, Computational biology, Genome, Viral, Biology, Virus, dna viruses, Article, Uncultivated virus genomes, Databases, 03 medical and health sciences, Annotation, Genetic, Virology, MD Multidisciplinary, Genetics, 030304 developmental biology, Human Genome, Biological classification, commitee, prediction, Metagenomics, Minimum Information about any (x) Sequence (MIxS), 030217 neurology & neurosurgery, discovery
Abstract: We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere., Nature Biotechnology, 37 (1), ISSN:1546-1696, ISSN:1087-0156
Published: 2018

32. The healthy human virome: from virus–host symbiosis to disease

Author: Valerian V. Dolja, Mart Krupovic, Eugene V. Koonin, National Center for Biotechnology Information (NCBI), Oregon State University (OSU), Virologie des archées - Archaeal Virology, Institut Pasteur [Paris], EVK is supported by the Intramural Research Program of the National Institutes of Health (National Library of Medicine). MK was supported by l’Agence Nationale de la Recherche grant ANR-20-CE20-0009., ANR-20-CE20-0009,VIROMET,Devoiler le virome des archées methanogenes(2020), and Institut Pasteur [Paris] (IP)
Subjects: 0301 basic medicine, viruses, 030106 microbiology, Endogenous retrovirus, Parasitism, Biology, Virus Replication, 03 medical and health sciences, Immune system, Virology, Humans, Human virome, Bacteriophages, Symbiosis, Mutualism (biology), Host (biology), Virome, biology.organism_classification, 3. Good health, Multicellular organism, 030104 developmental biology, Host-Pathogen Interactions, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Bacteria, Virus Physiological Phenomena
Abstract: International audience; Viruses are ubiquitous, essential components of any ecosystem, and of multicellular organism holobionts. Numerous viruses cause acute infection, killing the host or being cleared by immune system. In many other cases, viruses coexist with the host as symbionts, either temporarily or for the duration of the host's life. Apparently, virus-host relationships span the entire range from aggressive parasitism to mutualism. Here we attempt to delineate the healthy human virome, that is, the entirety of viruses that are present in a healthy human body. The bulk of the healthy virome consists of bacteriophages infecting bacteria in the intestine and other locations. However, a variety of viruses, such as anelloviruses and herpesviruses, and the numerous endogenous retroviruses, persist by replicating in human cells, and these are our primary focus. Crucially, the boundary between symbiotic and pathogenic viruses is fluid such that members of the healthy virome can become pathogens under changing conditions.
Published: 2021

33. Evolution of a major virion protein of the giant pandoraviruses from an inactivated bacterial glycoside hydrolase

Author: Natalya Yutin, Eugene V. Koonin, Mart Krupovic, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris], National Center for Biotechnology Information (NCBI), M.K. was supported by l’Agence Nationale de la Recherche Grant ANR-17-CE15-0005-01 (ENVIRA). N.Y. and E.V.K. are supported through the Intramural Research Program of the National Institutes of Health of the USA (National Library of Medicine)., ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), and Institut Pasteur [Paris] (IP)
Subjects: viruses, Pandoraviridae, Microbiology, Virus, 03 medical and health sciences, Virology, Gene duplication, Giant Virus, Gene, giant viruses, 030304 developmental biology, Genetics, virus evolution, 0303 health sciences, Pandoravirus, biology, 030306 microbiology, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, capsid protein, Capsid, Viral evolution, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, exaptation, glycoside hydrolase family 16, Research Article
Abstract: The diverse viruses in the phylum Nucleocytoviricota (also known as NLCDVs, Nucleo-cytoplasmic Large DNA Viruses) typically possess large icosahedral virions. However, in several families of Nucleocytoviricota, the icosahedral capsid was replaced by irregular particle shapes, most notably, the amphora-like virions of pandoraviruses and pithoviruses, the largest known virus particles in the entire virosphere. Pandoraviruses appear to be the most highly derived viruses in this phylum because their evolution involved not only the change in the virion shape, but also, the actual loss of the gene encoding double-jelly roll major capsid protein (DJR MCP), the main building block of icosahedral capsids in this virus assemblage. Instead, pandoravirus virions are built of unrelated abundant proteins. Here we show that the second most abundant virion protein of pandoraviruses, major virion protein 2 (MVP2), evolved from an inactivated derivative of a bacterial glycoside hydrolase of the GH16 family. The ancestral form of MVP2 was apparently acquired early in the evolution of the Nucleocytoviricota, to become a minor virion protein. After a duplication in the common ancestor of pandoraviruses and molliviruses, one of the paralogs displaces DJR MCP in pandoraviruses, conceivably, opening the way for a major increase in the size of the virion and the genome. Exaptation of a carbohydrate-binding protein for the function of the MVP is a general trend in virus evolution and might underlie the transformation of the virion shape in other groups of the Nucleocytoviricota as well.
Published: 2021

34. ELIXIR and Toxicology : a community in development

Author: Noelia Ramirez, Iseult Lynch, Nikolaos S. Thomaidis, Ralf J. M. Weber, Hilda Witters, Evan E Bolton, Antony Williams, Pavel Babica, Susanna-Assunta Sansone, Kasia Arturi, Anže Županič, Gerard J.P. van Westen, Karine Audouze, Sergio Martinez Cuesta, Tobias Schulze, Jos Bessems, Dimitrios Damalas, Montserrat Cases, Penny Nymark, Ferran Sanz, Uko Maran, Haralambos Sarimveis, Ludek Blaha, Jaroslav Slobodnik, Jos C. S. Kleinjans, Todor Kondic, Hristo Aladjov, Egon Willighagen, Hervé Ménager, Brett Sallach, Danyel Jennen, Sirarat Sarntivijai, Roland C. Grafström, Rob Stierum, Jonathan Tedds, John M. Hancock, Reza M. Salek, Boï Kone, Karel Berka, Herbert Oberacher, Craig E. Wheelock, Steffen Neumann, Alasdair J. G. Gray, Pascal Kahlem, Sylvie Remy, Emma L. Schymanski, Marco Dilger, Ola Spjuth, Barbara Zdrazil, Marvin Martens, Kirtan Dave, Jana Klánová, Henner Hollert, Daan P. Geerke, Philippe Rocca-Serra, Nina Jeliazkova, Thomas Exner, Chris T. Evelo, Fabien Jourdan, Reza Aalizadeh, Department of Bioinformatics, Maastricht University Medical Center (BiGCaT), The Netherlands Organisation for Applied Scientific Research (TNO), Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg [Luxembourg], Maastricht Centre for Systems Biology, Maastricht University Medical Center (MaCSBio), National and Kapodistrian University of Athens (NKUA), Bulgarian Academy of Sciences (BAS), Swiss Federal Institute of Aquatic Science & Technology (EAWA), Toxicité environnementale, cibles thérapeutiques, signalisation cellulaire (T3S - UMR_S 1124), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Research Centre for Toxic Compounds in the Environment [Brno] (RECETOX / MUNI), Faculty of Science [Brno] (SCI / MUNI), Masaryk University [Brno] (MUNI)-Masaryk University [Brno] (MUNI), Palacky University Olomouc, Flemish Institute for Technological Research (VITO), National Center for Biotechnology Information (NCBI), Chemotargets SL, GSFC University, Forschungs- und Beratungsinstitut Gefahrstoffe GmbH (FoBiG), Seven Past Nine, Vrije Universiteit Amsterdam [Amsterdam] (VU), Karolinska Institutet [Stockholm], Misvik Biology, Heriot-Watt University [Edinburgh] (HWU), ELIXIR Hub [Cambridge], Goethe-University Frankfurt am Main, Ideaconsult, Maastricht University [Maastricht], ToxAlim (ToxAlim), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), MetaboHUB-MetaToul, MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Faculté de Médecine, de pharmacie et d’Odonto-Stomatologie [Bamako, Mali] (FMPOS), Université de Bamako, University of Birmingham [Birmingham], University of Tartu, AstraZeneca [Cambridge, UK], Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Institut Français de Bioinformatique (IFB-CORE), Institut National de Recherche en Informatique et en Automatique (Inria)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Leibniz Institute of Plant Biochemistry (IPB), Innsbruck Medical University = Medizinische Universität Innsbruck (IMU), Universitat Rovira i Virgili, University of Oxford, Centre International de Recherche contre le Cancer - International Agency for Research on Cancer (CIRC - IARC), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), University of York [York, UK], Universitat Pompeu Fabra [Barcelona] (UPF), National Technical University of Athens [Athens] (NTUA), Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), Environmental Institute Kos, Uppsala University, Leiden Academic Center for Drug Research, United States Environmental Protection Agency [Cincinnati], University of Vienna [Vienna], National Institute of Biology [Ljubljana] (NIB), This work received funding from the European Union’s Horizon 2020 research infrastrcuture programme via the OpenRiskNet project under grant agreement No. 731075.This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 681002 (EU-ToxRisk).This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 814572.SN acknowledges BMBF funding under grant number 031L0107.This work was supported by OBERON (https://oberon-4eu.com), a project funded by the European Union's Horizon 2020 research and innovation program under the grant agreement No. 825712.This work was supported by the European Union,'s Horizon 2020 research and innovation program HBM4EU, grant agreement No. 733032 (https://www.hbm4eu.eu).Supported by the European Union’s Horizon 2020 programme under the Marie Skłodowska-Curie grant agreement No. 859891.Where authors are identified as personnel of the International Agency for Research on Cancer/World Health Organization, the authors alone are responsible for the views expressed in this article, and they do not necessarily represent the decisions, policy, or views of the International Agency for Research on Cancer/World Health Organization.This work was supported by the European Union,'s Horizon 2020 research and innovation program HARMLESS, grant agreement No. 953183.This work was supported by the European Union,'s Horizon 2020 research and innovation program Gov4Nano, grant agreement No. 814401.This work was supported by the Swedish Fund for Research Without Animal Experiments under grant number N2020-0005.This work was supported by the European Union,'s Horizon 2020 research and innovation program NTS-EXPOSURE, Grant agreement ID: 896141.This work was supported by the European Union,'s LIFE program LIFE-APEX, Grant agreement ID: LIFE17 ENV/SK/000355.This study was funded by the German Environment Agency within the PHION project (grant number 3718 674150).The Data Readiness Group is supported, in this ELIXIR Community, by the H2020 Precision Toxicology project (H2020-EU 965406).The Data Readiness Group is supported, in this ELIXIR Community, by the Wellcome ISA-InterMine project (208381/A/17/Z).The Data Readiness Group is supported, in this ELIXIR Community, by the Wellcome FAIRsharing project (212930/Z/18/Z).This work received funding from the European Union’s Horizon 2020 research and innovation programme RiskGONE Project under grant agreement No. 814425.NR's research is funded by a Miguel Servet contract (CO19/00060) from Instituto de Salud Carlos III, cofinanced by the European Union.UM (Uni. of Tartu) is grateful for support to Ministry of Education and Research, Republic of Estonia through Estonian Research Council (grant number IUT34-14) and to European Union European Regional Development Fund through Foundation Archimedes (grant number TK143, Centre of Excellence in Molecular Cell Engineering).Development and Implementation of a Sustainable Modelling Platform for NanoInformatics.Linking LRI Ambit chemoinformatic system with the IUCLID substance database to support read-across of substance endpoint data and category formation.This work was supported by the French Ministry of Research and National Research Agency as part of the French MetaboHUB, the national metabolomics and fluxomics infrastructure (Grant ANR-INBS-0010).This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement GOLIATH No. 825489., ANR-11-INBS-0010,METABOHUB,Développement d'une infrastructure française distribuée pour la métabolomique dédiée à l'innovation(2011), European Project: 681002,H2020,H2020-PHC-2015-single-stage_RTD,EU-ToxRisk(2016), European Project: 825712,H2020-EU.3.1.1. - Understanding health, wellbeing and disease,H2020-SC1-2018-Single-Stage-RTD,OBERON(2019), European Project: 733032,H2020,HBM4EU(2017), European Project: 814425,RiskGONE, European Project: 825489,H2020,GOLIATH(2019), Université de Toulouse (UT)-Ecole d'Ingénieurs de Purpan (INP - PURPAN), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ménager, Hervé, Développement d'une infrastructure française distribuée pour la métabolomique dédiée à l'innovation - - METABOHUB2011 - ANR-11-INBS-0010 - INBS - VALID, An Integrated European ‘Flagship’ Program Driving Mechanism-based Toxicity Testing and Risk Assessment for the 21st Century - EU-ToxRisk - - H20202016-01-01 - 2021-12-31 - 681002 - VALID, An integrative strategy of testing systems for identification of EDs related to metabolic disorders - OBERON - - H2020-EU.3.1.1. - Understanding health, wellbeing and disease2019-01-01 - 2019-12-31 - 825712 - VALID, European Human Biomonitoring Initiative - HBM4EU - - H20202017-01-01 - 2021-12-31 - 733032 - VALID, Risk Governance of Nanotechnology - RiskGONE - 814425 - INCOMING, and Beating Goliath: Generation Of NoveL, Integrated and Internationally Harmonised Approaches for Testing Metabolism Disrupting Compounds - GOLIATH - - H20202019-01-19 - 2023-12-31 - 825489 - VALID
Subjects: Interoperability, Context (language use), interoperability, Predictive toxicology, Multidisciplinary, general & others [F99] [Life sciences], Pharmacology and Toxicology, 010501 environmental sciences, Toxicology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Multidisciplinaire, généralités & autres [F99] [Sciences du vivant], General Pharmacology, Toxicology and Pharmaceutics, Chemical risk, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], 030304 developmental biology, 0105 earth and related environmental sciences, computer.programming_language, FAIR, 0303 health sciences, Government, General Immunology and Microbiology, General Medicine, Farmakologi och toxikologi, Sketch, 3. Good health, ELIXIR, [SDV.TOX] Life Sciences [q-bio]/Toxicology, [SDV.TOX]Life Sciences [q-bio]/Toxicology, Elixir (programming language), [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], computer
Abstract: International audience; Toxicology has been an active research field for many decades, with academic, industrial and government involvement. Modern omics and computational approaches are changing the field, from merely disease-specific observational models into target-specific predictive models. Traditionally, toxicology has strong links with other fields such as biology, chemistry, pharmacology and medicine. With the rise of synthetic and new engineered materials, alongside ongoing prioritisation needs in chemical risk assessment for existing chemicals, early predictive evaluations are becoming of utmost importance to both scientific and regulatory purposes. ELIXIR is an intergovernmental organisation that brings together life science resources from across Europe. To coordinate the linkage of various life science efforts around modern predictive toxicology, the establishment of a new ELIXIR Community is seen as instrumental. In the past few years, joint efforts, building on incidental overlap, have been piloted in the context of ELIXIR. For example, the EU-ToxRisk, diXa, HeCaToS, transQST, and the nanotoxicology community have worked with the ELIXIR TeSS, Bioschemas, and Compute Platforms and activities. In 2018, a core group of interested parties wrote a proposal, outlining a sketch of what this new ELIXIR Toxicology Community would look like. A recent workshop (held September 30th to October 1st, 2020) extended this into an ELIXIR Toxicology roadmap and a shortlist of limited investment-high gain collaborations to give body to this new community. This Whitepaper outlines the results of these efforts and defines our vision of the ELIXIR Toxicology Community and how it complements other ELIXIR activities.
Published: 2021

35. Dog10K_Boxer_Tasha_1.0: A Long-Read Assembly of the Dog Reference Genome

Author: Xiangquan Zhang, Christophe Hitte, Elaine A. Ostrander, Patrick Masterson, Terence Murphy, Yan-Hu Liu, Jeffrey M. Kidd, S. Emery, Brian W. Davis, Tosso Leeb, Ya-Ping Zhang, Reuben M. Buckley, Guo-Dong Wang, Vidhya Jagannathan, University of Bern, Institut de Génétique et Développement de Rennes (IGDR), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), University of Michigan [Ann Arbor], University of Michigan System, National Center for Biotechnology Information (NCBI), Texas A&M University [College Station], National Human Genome Research Institute (NHGRI), Kunming Institute of Zoology, Chinese Academy of Sciences [Beijing] (CAS), 2019YFA0707101, The National Key R&D Program of China, R01GM140135, National Institutes of Health, Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), and Kunming Institute of Zoology (KIZ)
Subjects: clone (Java method), 0301 basic medicine, Canis lupus familiaris, contiguity, 0206 medical engineering, Sequence assembly, 610 Medicine & health, 02 engineering and technology, Computational biology, QH426-470, Biology, resource, Article, Contig Mapping, 03 medical and health sciences, Annotation, high quality, Dogs, 0302 clinical medicine, Pacific biosciences, Genetics, Animals, Canine genetics, Gene, Genetics (clinical), 030304 developmental biology, 0303 health sciences, Genome, 630 Agriculture, Shotgun sequencing, Molecular Sequence Annotation, Gene Annotation, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, 030104 developmental biology, annotation, 590 Animals (Zoology), 570 Life sciences, biology, 020602 bioinformatics, 030217 neurology & neurosurgery, Reference genome
Abstract: The domestic dog has evolved to be an important biomedical model for studies regarding the genetic basis of disease, morphology and behavior. Genetic studies in the dog have relied on a draft reference genome of a purebred female boxer dog named “Tasha” initially published in 2005. Derived from a Sanger whole genome shotgun sequencing approach coupled with limited clone-based sequencing, the initial assembly and subsequent updates have served as the predominant resource for canine genetics for 15 years. While the initial assembly produced a good-quality draft, as with all assemblies produced at the time, it contained gaps, assembly errors and missing sequences, particularly in GC-rich regions, which are found at many promoters and in the first exons of protein-coding genes. Here, we present Dog10K_Boxer_Tasha_1.0, an improved chromosome-level highly contiguous genome assembly of Tasha created with long-read technologies that increases sequence contiguity &gt, 100-fold, closes &gt, 23,000 gaps of the CanFam3.1 reference assembly and improves gene annotation by identifying &gt, 1200 new protein-coding transcripts. The assembly and annotation are available at NCBI under the accession GCF_000002285.5.
Published: 2021
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36. Adnaviria: a New Realm for Archaeal Filamentous Viruses with Linear A-Form Double-Stranded DNA Genomes

Author: Edward H. Egelman, Diana P. Baquero, Fengbin Wang, Eugene V. Koonin, Valerian V. Dolja, David Prangishvili, Jens H. Kuhn, Mart Krupovic, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris] (IP), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Department of Biochemistry and Molecular Genetics [Charlottesville], University of Virginia, Department of Botany and Plant Pathology, Oregon State University (OSU), National Library of Medicine (NLM), National Institutes of Health [Bethesda] (NIH)-National Center for Biotechnology Information (NCBI), M.K. was supported by l’Agence Nationale de la Recherche (grant ANR-20-CE20-0009-02) and Emergence(s) project MEMREMA from the Ville de Paris. E.V.K. is supported by the Intramural Research Program of the U.S. National Institutes of Health (National Library of Medicine). E.H.E. was supported by NIH grant R35GM122510. This work was supported in part through a Laulima Government Solutions, LLC, prime contract with the U.S. NIAID under contract no. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC, under contract no. HHSN272201800013C., ANR-20-CE20-0009,VIROMET,Devoiler le virome des archées methanogenes(2020), Institut Pasteur [Paris], and University of Virginia [Charlottesville]
Subjects: viruses, Immunology, Rudiviridae, virus taxonomy, Microbiology, Genome, Lipothrixviridae, 03 medical and health sciences, Monophyly, chemistry.chemical_compound, Virology, major capsid protein, virus classification, Virus classification, 030304 developmental biology, virus evolution, 0303 health sciences, International Committee on Taxonomy of Viruses (ICTV), Tokiviricetes, biology, 030306 microbiology, virus structure and assembly, Tristromaviridae, biology.organism_classification, Ligamenvirales, hyperthermophilic archaea, chemistry, Evolutionary biology, Insect Science, Viral evolution, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Commentary, A-form DNA, DNA
Abstract: International audience; The International Committee on Taxonomy of Viruses (ICTV) has recently adopted a comprehensive, hierarchical system of virus taxa. The highest ranks in this hierarchy are realms, each of which is considered monophyletic but apparently originated independently of other realms. Here, we announce the creation of a new realm, Adnaviria, which unifies archaeal filamentous viruses with linear A-form double-stranded DNA genomes and characteristic major capsid proteins unrelated to those encoded by other known viruses.
Published: 2021

37. Findings of the WMT 2021 Biomedical Translation Shared Task: Summaries of Animal Experiments as New Test Set

Author: Yeganova, Lana, Wiemann, Dina, Neves, Mariana, Vezzani, Federica, Siu, Amy, Unanue, Iñigo, Oronoz, Maite, Mah, Nancy, Névéol, Aurélie, Martinez, David, Bawden, Rachel, Di Maria Di Nunzo, Giorgio, Roller, Roland, Thomas, Philippe, Grozea, Cristian, Perez De Viñaspre, Olatz, Navarro, Maria Vicente, Yepes, Antonio, Laboratoire Interdisciplinaire des Sciences du Numérique (LISN), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Information, Langue Ecrite et Signée (ILES), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Sciences et Technologies des Langues (STL), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), National Center for Biotechnology Information (NCBI), Novartis Pharma AG, German Federal Institute for Risk Assessment [Berlin] (BfR), Azienda Ospedale Università di Padova = Hospital-University of Padua (AOUP), Berliner Hochschule für Technik (BHT), University of Technology Sydney (UTS), University of the Basque Country/Euskal Herriko Unibertsitatea (UPV/EHU), Fraunhofer Institute for Biomedical Engineering [Sulzbach] (Fraunhofer IBMT), Fraunhofer (Fraunhofer-Gesellschaft), Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Sciences et Technologies des Langues (STL), Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), University of Melbourne, Automatic Language Modelling and ANAlysis & Computational Humanities (ALMAnaCH), Inria de Paris, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Deutsches Forschungszentrum für Künstliche Intelligenz GmbH = German Research Center for Artificial Intelligence (DFKI), Fraunhofer Institute for Open Communication Systems (Fraunhofer FOKUS), and Maika Spanish Translator
Subjects: [INFO.INFO-CL]Computer Science [cs]/Computation and Language [cs.CL]
Abstract: International audience; In the sixth edition of the WMT Biomedical Task, we addressed a total of eight language pairs, namely English/German, English/French, English/Spanish, English/Portuguese, English/Chinese, English/Russian, English/Italian, and English/Basque. Further, our tests were composed of three types of textual test sets. New to this year, we released a test set of summaries of animal experiments, in addition to the test sets of scientific abstracts and terminologies. We received a total of 107 submissions from 15 teams from 6 countries.
Published: 2021

38. Rfam 14: expanded coverage of metagenomic, viral and microRNA families

Author: Joanna Argasinska, Sean R. Eddy, Ioanna Kalvari, Elena Rivas, Anton I. Petrov, Kevin Lamkiewicz, Alex Bateman, Robert D. Finn, Daniel Gautheret, Sam Griffiths-Jones, Manja Marz, Nancy Ontiveros-Palacios, Eric P. Nawrocki, Zasha Weinberg, Claire Toffano-Nioche, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, National Center for Biotechnology Information (NCBI), Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], European Virus Bioinformatics Center [Jena], University of Manchester [Manchester], Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Séquence, Structure et Fonction des ARN (SSFA), Département Biologie des Génomes (DBG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Interdisciplinary Centre for Bioinformatics [Leipzig] (IZBI), Universität Leipzig, Harvard University, Harvard John A. Paulson School of Engineering and Applied Sciences (SEAS), Howard University, Universität Leipzig [Leipzig], and Harvard University [Cambridge]
Subjects: RNA, Untranslated, AcademicSubjects/SCI00010, Sequence analysis, [SDV]Life Sciences [q-bio], Rfam, Computational biology, Biology, MiRBase, 03 medical and health sciences, Annotation, microRNA, Genetics, Database Issue, Humans, Base Pairing, 030304 developmental biology, Internet, 0303 health sciences, Multiple sequence alignment, Bacteria, Base Sequence, Sequence Analysis, RNA, 030302 biochemistry & molecular biology, Molecular Sequence Annotation, MicroRNAs, RNA, Bacterial, Metagenomics, Viruses, Metagenome, Nucleic Acid Conformation, RNA, Viral, Databases, Nucleic Acid, Sequence Alignment, Software
Abstract: Rfam is a database of RNA families where each of the 3444 families is represented by a multiple sequence alignment of known RNA sequences and a covariance model that can be used to search for additional members of the family. Recent developments have involved expert collaborations to improve the quality and coverage of Rfam data, focusing on microRNAs, viral and bacterial RNAs. We have completed the first phase of synchronising microRNA families in Rfam and miRBase, creating 356 new Rfam families and updating 40. We established a procedure for comprehensive annotation of viral RNA families starting with Flavivirus and Coronaviridae RNAs. We have also increased the coverage of bacterial and metagenome-based RNA families from the ZWD database. These developments have enabled a significant growth of the database, with the addition of 759 new families in Rfam 14. To facilitate further community contribution to Rfam, expert users are now able to build and submit new families using the newly developed Rfam Cloud family curation system. New Rfam website features include a new sequence similarity search powered by RNAcentral, as well as search and visualisation of families with pseudoknots. Rfam is freely available at https://rfam.org.
Published: 2020
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39. Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome

Author: Michael J. Bocek, Andrew Fire, Yuri I. Wolf, Yongjie Wang, Mart Krupovic, Valerian V. Dolja, Shuang Wu, Darius Kazlauskas, Sukrit Silas, Eugene V. Koonin, National Library of Medicine (NLM), National Institutes of Health [Bethesda] (NIH)-National Center for Biotechnology Information (NCBI), Department of Cellular and Molecular Pharmacology [San Francisco] (CMP), University of California [San Francisco] (UCSF), University of California-University of California, College of Food Science and Technology [Shangai], Shanghai Ocean University, Qingdao National Laboratory for Marine Science and Technology, Institute of Biotechnology [Vilnius], Life Science Center [Vilnius], Vilnius University [Vilnius]-Vilnius University [Vilnius], Virologie des archées - Archaeal Virology, Institut Pasteur [Paris], Department of Pathology [Stanford], Stanford Medicine, Stanford University-Stanford University, Department of Botany and Plant Pathology, Oregon State University (OSU), Y.I.W. and E.V.K. are supported through the Intramural Research Program of the US National Institutes of Health (National Library of Medicine). S.S. is a Damon Runyon Fellow supported by the Damon Runyon Cancer Research Foundation (DRG-(2352-19)). A.F. was supported by National Institutes of Health awards R01GM37706 and R35GM130366. M.K. was supported by l’Agence Nationale de la Recherche grant ANR-17-CE15-0005-01 (ENVIRA). D.K. was funded by the European Social Fund under no. 09.3.3-LMT-K-712 ‘Development of Competences of Scientists, other Researchers and Students through Practical Research Activities’ measure. Y.W. was supported by the National Natural Science Foundation of China (nos. 41376135, 31570112 and 41876195)., We thank N. Yutin for providing protein multiple-sequence analysis for DNA virus search., ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), University of California [San Francisco] (UC San Francisco), University of California (UC)-University of California (UC), and Institut Pasteur [Paris] (IP)
Subjects: Microbiology (medical), Water microbiology, China, viruses, Immunology, Genome, Viral, Applied Microbiology and Biotechnology, Microbiology, Article, Evolution, Molecular, Microbial ecology, 03 medical and health sciences, chemistry.chemical_compound, Viral Proteins, Capping enzyme, Plant virus, RNA polymerase, Gene Order, Genetics, RNA Viruses, Human virome, Amino Acid Sequence, Phylogeny, 030304 developmental biology, 0303 health sciences, biology, single-stranded-DNA, genome organization, nucleotide-sequence, diversity, discovery, plant, identification, virosphere, phylogeny, evolution, 030306 microbiology, Potyviridae, RNA, Computational Biology, RNA virus, Cell Biology, Biodiversity, biology.organism_classification, Marnaviridae, Computational biology and bioinformatics, chemistry, Evolutionary biology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Metagenome, Metagenomics
Abstract: RNA viruses in aquatic environments remain poorly studied. Here, we analysed the RNA virome from approximately 10 l water from Yangshan Deep-Water Harbour near the Yangtze River estuary in China and identified more than 4,500 distinct RNA viruses, doubling the previously known set of viruses. Phylogenomic analysis identified several major lineages, roughly, at the taxonomic ranks of class, order and family. The 719-member-strong Yangshan virus assemblage is the sister clade to the expansive class Alsuviricetes and consists of viruses with simple genomes that typically encode only RNA-dependent RNA polymerase (RdRP), capping enzyme and capsid protein. Several clades within the Yangshan assemblage independently evolved domain permutation in the RdRP. Another previously unknown clade shares ancestry with Potyviridae, the largest known plant virus family. The ‘Aquatic picorna-like viruses/Marnaviridae’ clade was greatly expanded, with more than 800 added viruses. Several RdRP-linked protein domains not previously detected in any RNA viruses were identified, such as the small ubiquitin-like modifier (SUMO) domain, phospholipase A2 and PrsW-family protease domain. Multiple viruses utilize alternative genetic codes implying protist (especially ciliate) hosts. The results reveal a vast RNA virome that includes many previously unknown groups. However, phylogenetic analysis of the RdRPs supports the previously established five-branch structure of the RNA virus evolutionary tree, with no additional phyla., Metagenomic analysis of a single RNA virome from the Yangshan Deep-Water Harbour in China enabled the recovery of more than 4,500 distinct RNA viruses, doubling the known set of RNA viruses to date, and provided insights into their biology.
Published: 2020

40. The replication machinery of LUCA: common origin of DNA replication and transcription

Author: Eugene V. Koonin, Mart Krupovic, Yoshizumi Ishino, Sonoko Ishino, National Library of Medicine (NLM), National Institutes of Health [Bethesda] (NIH)-National Center for Biotechnology Information (NCBI), Virologie des archées - Archaeal Virology, Institut Pasteur [Paris], Department of Bioscience and Biotechnology [Fukuoka], Graduate School of Bioresource and Bioenvironmental Sciences [Fukuoka], Kyushu University [Fukuoka]-Kyushu University [Fukuoka], EVK is supported through the Intramural Research Program of the National Institutes of Health of the USA. MK was supported by l’Agence Nationale de la Recherche (project ENVIRA, no. ANR-17-CE15-0005-01)., EVK is grateful to Dr. Purificación López-García for the valuable discussions, ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), Institut Pasteur [Paris] (IP), and Kyushu University-Kyushu University
Subjects: DNA Replication, Opinion, Transcription, Genetic, Physiology, DNA polymerase, [SDV]Life Sciences [q-bio], Plant Science, General Biochemistry, Genetics and Molecular Biology, Homology (biology), Evolution, Molecular, 03 medical and health sciences, chemistry.chemical_compound, Structural Biology, Transcription (biology), Three-domain system, RNA polymerase, Homologous chromosome, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, lcsh:QH301-705.5, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Genetics, 0303 health sciences, biology, Bacteria, 030306 microbiology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], DNA replication, Eukaryota, Cell Biology, biology.organism_classification, Archaea, Biological Evolution, lcsh:Biology (General), chemistry, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, biology.protein, General Agricultural and Biological Sciences, Developmental Biology, Biotechnology
Abstract: Origin of DNA replication is an enigma because the replicative DNA polymerases (DNAPs) are not homologous among the three domains of life, Bacteria, Archaea, and Eukarya. The homology between the archaeal replicative DNAP (PolD) and the large subunits of the universal RNA polymerase (RNAP) responsible for transcription suggests a parsimonious evolutionary scenario. Under this model, RNAPs and replicative DNAPs evolved from a common ancestor that functioned as an RNA-dependent RNA polymerase in the RNA-protein world that predated the advent of DNA replication. The replicative DNAP of the Last Universal Cellular Ancestor (LUCA) would be the ancestor of the archaeal PolD.
Published: 2020

41. Cressdnaviricota : a Virus Phylum Unifying Seven Families of Rep-Encoding Viruses with Single-Stranded, Circular DNA Genomes

Author: Eric Delwart, Mya Breitbart, F. Murilo Zerbini, Karyna Rosario, Yuri I. Wolf, Eugene V. Koonin, Mart Krupovic, Natalya Yutin, Valerian V. Dolja, Darius Kazlauskas, Jens H. Kuhn, Arvind Varsani, Balázs Harrach, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris], School of Life Sciences [Tempe, USA], Arizona State University [Tempe] (ASU), Department of Integrative Biomedical Sciences [Cape Town], University of Cape Town, Life Science Center [Vilnius], Vilnius University [Vilnius], College of Marine Science [St Petersburg, FL], University of South Florida [Tampa] (USF), Vitalant Research Institute [San Francisco], Department of Laboratory Medicine [San Francisco], University of California [San Francisco] (UCSF), University of California-University of California, National Library of Medicine (NLM), National Institutes of Health [Bethesda] (NIH)-National Center for Biotechnology Information (NCBI), Institute for Veterinary Medical Research [Budapest] (AOTI), Centre for Agricultural Research [Budapest] (ATK), Hungarian Academy of Sciences (MTA)-Hungarian Academy of Sciences (MTA), Universidade Federal de Vicosa (UFV), Department of Botany and Plant Pathology, Oregon State University (OSU), Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), M.K. was supported by l’Agence Nationale de la Recherche (project ENVIRA, no. ANR-17-CE15-0005-01). E.V.K., Y.I.W., and N.Y. are supported by the Intramural Research Program of the U.S. National Institutes of Health (National Library of Medicine). B.H. was supported by the Hungarian National Research, Development, and Innovation Office (NN128309). This work was supported in part through the Laulima Government Solutions, LLC, prime contract with the U.S. National Institute of Allergy and Infectious Diseases (NIAID) under contract no. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC, under contract no. HHSN272201800013C., ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), Institut Pasteur [Paris] (IP), University of California [San Francisco] (UC San Francisco), University of California (UC)-University of California (UC), and Universidade Federal de Viçosa = Federal University of Viçosa (UFV)
Subjects: Immunology, CRESS DNA viruses, Smacoviridae, Microbiology, Genome, Virus, 03 medical and health sciences, Virology, Geminiviridae, virus classification, Letter to the Editor, Virus classification, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetics, Redondoviridae, Circoviridae, virus evolution, 0303 health sciences, International Committee on Taxonomy of Viruses (ICTV), biology, 030306 microbiology, Phylum, Bacilladnaviridae, Genomoviridae, Nanoviridae, biology.organism_classification, Insect Science, Viral evolution, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING
Abstract: International audience; Letter to the Editor
Published: 2020

42. Global Organization and Proposed Megataxonomy of the Virus World

Author: Yuri I. Wolf, Eugene V. Koonin, Mart Krupovic, Valerian V. Dolja, Natalya Yutin, F. Murilo Zerbini, Arvind Varsani, Jens H. Kuhn, National Library of Medicine (NLM), National Institutes of Health [Bethesda] (NIH)-National Center for Biotechnology Information (NCBI), Department of Botany and Plant Pathology, Oregon State University (OSU), Virologie des archées - Archaeal Virology, Institut Pasteur [Paris] (IP), School of Life Sciences [Tempe, USA], Arizona State University [Tempe] (ASU), University of Cape Town, Universidade Federal de Viçosa = Federal University of Viçosa (UFV), Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), E.V.K., Y.I.W., and N.Y. are supported by the Intramural Research Program of the U.S. National Institutes of Health (National Library of Medicine). M.K. was supported by l’Agence Nationale de la Recherche (project ENVIRA, no. ANR-17-CE15-0005-01). J.H.K. is supported through Battelle Memorial Institute’s prime contract with the U.S. National Institute of Allergy and Infectious Diseases (NIAID) under contract no. HHSN272200700016I., We thank Jiro Wada (Integrated Research Facility at Fort Detrick) for help with figure preparation., ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), Institut Pasteur [Paris], and Universidade Federal de Vicosa (UFV)
Subjects: DNA Replication, realm, Genes, Viral, viruses, megataxonomy, virus nomenclature, Genome, Viral, Review, Biology, phylogeny, virus taxonomy, Microbiology, Genome, Virus, Evolution, Molecular, 03 medical and health sciences, chemistry.chemical_compound, ICTV, RNA polymerase, evolution, RNA Viruses, virus classification, Molecular Biology, Gene, Virus classification, 030304 developmental biology, virosphere, 0303 health sciences, 030306 microbiology, DNA Viruses, RNA, phylogenomics, Reverse transcriptase, Infectious Diseases, chemistry, Viral replication, Evolutionary biology, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Virus Physiological Phenomena
Abstract: International audience; SUMMARY : Viruses and mobile genetic elements are molecular parasites or symbionts that coevolve with nearly all forms of cellular life. The route of virus replication and protein expression is determined by the viral genome type. Comparison of these routes led to the classification of viruses into seven "Baltimore classes" (BCs) that define the major features of virus reproduction. However, recent phylogenomic studies identified multiple evolutionary connections among viruses within each of the BCs as well as between different classes. Due to the modular organization of virus genomes, these relationships defy simple representation as lines of descent but rather form complex networks. Phylogenetic analyses of virus hallmark genes combined with analyses of gene-sharing networks show that replication modules of five BCs (three classes of RNA viruses and two classes of reverse-transcribing viruses) evolved from a common ancestor that encoded an RNA-directed RNA polymerase or a reverse transcriptase. Bona fide viruses evolved from this ancestor on multiple, independent occasions via the recruitment of distinct cellular proteins as capsid subunits and other structural components of virions. The single-stranded DNA (ssDNA) viruses are a polyphyletic class, with different groups evolving by recombination between rolling-circle-replicating plasmids, which contributed the replication protein, and positive-sense RNA viruses, which contributed the capsid protein. The double-stranded DNA (dsDNA) viruses are distributed among several large monophyletic groups and arose via the combination of distinct structural modules with equally diverse replication modules. Phylogenomic analyses reveal the finer structure of evolutionary connections among RNA viruses and reverse-transcribing viruses, ssDNA viruses, and large subsets of dsDNA viruses. Taken together, these analyses allow us to outline the global organization of the virus world. Here, we describe the key aspects of this organization and propose a comprehensive hierarchical taxonomy of viruses.
Published: 2020

43. Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

Author: Adriaenssens, Evelien M, Sullivan, Matthew B, Knezevic, Petar, van Zyl, Leonardo J, Sarkar, B L, Dutilh, Bas E, Alfenas-Zerbini, Poliane, Łobocka, Małgorzata, Tong, Yigang, Brister, James Rodney, Moreno Switt, Andrea I, Klumpp, Jochen, Aziz, Ramy Karam, Barylski, Jakub, Uchiyama, Jumpei, Kropinski, Andrew M, Petty, Nicola K, Clokie, Martha R J, Kushkina, Alla I, Morozova, Vera V, Duffy, Siobain, Gillis, Annika, Rumnieks, Janis, Kurtböke, İpek, Chanishvili, Nina, Goodridge, Lawrence, Wittmann, Johannes, Lavigne, Rob, Jang, Ho Bin, Prangishvili, David, Enault, Francois, Turner, Dann, Poranen, Minna M, Oksanen, Hanna M, Krupovic, Mart, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Quadram Institute, Biotechnology and Biological Sciences Research Council (BBSRC), Department of Civil, Environmental and Geodetic Engineering [Columbus, USA] (CEGE), Ohio State University [Columbus] (OSU), University of Novi Sad, Institute for Microbial Biotechnology and Metagenomics [Cape Town, South Africa] (IMBM), University of the Western Cape (UWC), National Institute of Cholera and Enteric Diseases, Theoretical Biology and Bioinformatics [Utrecht, The Netherlands], Utrecht University [Utrecht], Radboud University Medical Center [Nijmegen], Universidade Federal de Viçosa = Federal University of Viçosa (UFV), Institute of Biochemistry & Biophysics, Polish Academy of Sciences (PAN), Beijing University of Chemical Technology, National Library of Medicine (NLM), National Institutes of Health [Bethesda] (NIH)-National Center for Biotechnology Information (NCBI), Universidad Andrés Bello [Santiago] (UNAB), Institute of Food, Nutrition and Health [Zurich, Suisse] (IFNH), Department of Health Sciences and Technology [ETH Zürich] (D-HEST), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)- Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Cairo University, Adam Mickiewicz University in Poznań (UAM), Azabu University, San Diego State University (SDSU), University of Guelph, Ontario Veterinary College [Univ. Guelph, Canada], iThree Institute, University of Technology Sydney (UTS), University of Leicester, D.K. Zabolotny Institute of Microbiology and Virology [Kyiv, Ukraine], National Academy of Sciences of Ukraine (NASU), Institute of Chemical Biology and Fundamental Medicine [Novosibirsk, Russia] (ICBFM SB RAS), Siberian Branch of the Russian Academy of Sciences (SB RAS), Rutgers University [Newark], Rutgers University System (Rutgers), Imperial College London, Latvian Biomedical Research and Study Centre [Rīga], University of the Sunshine Coast (USC), George Eliava Institute of Bacteriophages, Microbiology and Virology [Tbilisi, Georgia], Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ), Department of Biosystems (BIOSYST), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Virologie des archées - Archaeal Virology, Institut Pasteur [Paris] (IP), Ivane Javakhishvili Tbilisi State University (TSU), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Faculty of Health and Applied Sciences [Bristol, UK], University of the West of England [Bristol] (UWE Bristol), Faculty of Biological and Environmental Sciences [Helsinki], Helsingin yliopisto = Helsingfors universitet = University of Helsinki, This research was funded by the BBSRC Institute Strategic Programme Gut Microbes and Health BB/R012490/1 and its constituent project(s) BBS/E/F/000PR10353. B.E.D. was supported by the Netherlands Organization for Scientific Research (NWO), Vidi Grant 864.14.004. R.A.E was supported by Grant MCB-1330800 from the National Science Foundation. J.R.B. was supported by the Intramural Research Program of the National Institutes of Health, National Library of Medicine. R.L. is a member of the PhageBiotics Research Community, supported by FWO Vlaanderen. M.M.P. was supported by the Academy of Finland (272507). H.M.O. was supported by University of Helsinki funding for Instruct-F1 research infrastructure., The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies of their organizations. E.M.A gratefully acknowledges the support of the UK Biotechnology and Biological Sciences Research Council (BBSRC)., UCL - SST/ELI/ELIM - Applied Microbiology, University of the Western Cape, Universidade Federal de Vicosa (UFV), Universidad Andrés Bello - UNAB (CHILE), Institut Pasteur [Paris], University of Helsinki, and Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])
Subjects: 06 Biological Sciences, 07 Agricultural and Veterinary Sciences, 11 Medical and Health Sciences, Archaeal Viruses, 0303 health sciences, MESH: Bacteriophages/classification, Bacteria, 030306 microbiology, MESH: Bacteria/virology, Coronacrisis-Taverne, General Medicine, Classification, MESH: Archaeal Viruses/classification, Archaea, 03 medical and health sciences, All institutes and research themes of the Radboud University Medical Center, Virology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14], Bacteriophages, MESH: Archaea/virology, MESH: Classification/methods, 030304 developmental biology
Abstract: International audience; This article is a summary of the activities of the ICTV's Bacterial and Archaeal Viruses Subcommittee for the years 2018 and 2019. Highlights include the creation of a new order, 10 families, 22 subfamilies, 424 genera and 964 species. Some of our concerns about the ICTV's ability to adjust to and incorporate new DNA- and protein-based taxonomic tools are discussed.
Published: 2020

44. Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest

Author: J. Spencer Johnston, John H. Werren, Hugh M. Robertson, Joshua B. Benoit, Shannon Dugan, Monica Munoz-Torres, Richard A. Gibbs, Kim C. Worley, Raman Bansal, Patrick Masterson, Joshua H. Rhoades, Panagiotis Ioannidis, Christopher P. Childers, Dawn E. Gundersen-Rindal, Yi Han, Brent A. Kronmiller, Alexander G. Martynov, Brenda Oppert, Harshavardhan Doddapaneni, Stephen Richards, Zhijian Jake Tu, Richard W. Hardy, Christopher J. Holmes, Florian Maumus, Shwetha C. Murali, Markus Friedrich, Evgeny M. Zdobnov, Alys M. Cheatle Jarvela, Arun S. Velamuri, Mengyao Chen, Monica F. Poelchau, Matthew T. Weirauch, Michael E. Sparks, Robert M. Waterhouse, Katie Reding, Brantley Hall, Sandra L. Lee, Jiaxin Qu, Jeffery W. Jones, David W. Farrow, Kristen A. Panfilio, Adelaide C. Rhodes, Jackson Wells, Hsu Chao, Donna M. Muzny, Sammy Cheng, Huyen Dinh, David R. Nelson, Leslie Pick, Elena N. Elpidina, Michael B. Blackburn, Rose Richter, Daniel S.T. Hughes, Terence Murphy, Faith Kung, Andrew J. Rosendale, Débora P. Paula, Biochemistry, Ioannidis, Panagiotis, Zdobnov, Evgeny, Department of Biochemistry and Molecular Biology [Houston, TX, USA], The University of Texas Medical School at Houston, Human Genome Sequencing Center [Houston] (HGSC), Baylor College of Medicine (BCM), Baylor University-Baylor University, Human Genome Sequencing Center, Baylor College of Medicine, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Recherche Génomique Info (URGI), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), National Center for Biotechnology Information (NCBI), University of Tennessee, Department of Biology, Georgetown University, University of Illinois [Chicago] (UIC), University of Illinois System, Université de Lausanne (UNIL), Cincinnati Children's Hospital Medical Center, Department of Genetic Medicine and Development [Geneva], Université de Genève (UNIGE), Invasive Insect Biocontrol and Behavior Laboratory [Beltsville, USA], USDA Agricultural Research Service [Beltsville, Maryland], and USDA-ARS : Agricultural Research Service-USDA-ARS : Agricultural Research Service
Subjects: 0106 biological sciences, Integrated pest management, Gene Transfer, Insect, 01 natural sciences, Genome, Medical and Health Sciences, chemoreceptors, Invasive species, invasive species, Insecticide Resistance, Genome Size, ddc:576.5, ComputingMilieux_MISCELLANEOUS, Phylogeny, media_common, 0303 health sciences, biology, Ecology, Biological Sciences, Habitat, Insect Proteins, Brown marmorated stink bug genome, odorant binding proteins, Biotechnology, Research Article, lcsh:QH426-470, Gene Transfer, Horizontal, Bioinformatics, media_common.quotation_subject, lcsh:Biotechnology, 010603 evolutionary biology, Horizontal, Heteroptera, 03 medical and health sciences, lcsh:TP248.13-248.65, Information and Computing Sciences, Genetics, Animals, polyphagy, Brown marmorated stink bug, Ecosystem, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, QL, Whole Genome Sequencing, opsins, Human Genome, fungi, 15. Life on land, Pesticide, biology.organism_classification, Pentatomid genomics, lcsh:Genetics, PEST analysis, cathepsins, Introduced Species, xenobiotic detoxification
Abstract: BackgroundHalyomorpha halys(Stål), the brown marmorated stink bug, is a highly invasive insect species due in part to its exceptionally high levels of polyphagy. This species is also a nuisance due to overwintering in human-made structures. It has caused significant agricultural losses in recent years along the Atlantic seaboard of North America and in continental Europe. Genomic resources will assist with determining the molecular basis for this species’ feeding and habitat traits, defining potential targets for pest management strategies.ResultsAnalysis of the 1.15-Gb draft genome assembly has identified a wide variety of genetic elements underpinning the biological characteristics of this formidable pest species, encompassing the roles of sensory functions, digestion, immunity, detoxification and development, all of which likely supportH. halys’ capacity for invasiveness. Many of the genes identified herein have potential for biomolecular pesticide applications.ConclusionsAvailability of theH. halysgenome sequence will be useful for the development of environmentally friendly biomolecular pesticides to be applied in concert with more traditional, synthetic chemical-based controls.
Published: 2020

45. Evolutionary entanglement of mobile genetic elements and host defence systems: guns for hire

Author: Kira S. Makarova, Yuri I. Wolf, Mart Krupovic, Eugene V. Koonin, National Library of Medicine (NLM), National Institutes of Health [Bethesda] (NIH)-National Center for Biotechnology Information (NCBI), Virologie des archées - Archaeal Virology, Institut Pasteur [Paris], Département de Microbiologie - Department of Microbiology, E.V.K., K.S.M. and Y.I.W. are supported by the Intramural Research Program funds of the US National Institutes of Health (US Department of Health and Human Services). M.K. was supported by the Agence Nationale de la Recherche (France) project ENVIRA (no. ANR-17-CE15-0005-01)., E.V.K. thanks U. Gophna (Tel Aviv University) and E. Westra (University of Exeter) for inspiring discussions., ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), and Institut Pasteur [Paris] (IP)
Subjects: CRISPR-Cas systems, Gene Transfer, Horizontal, [SDV]Life Sciences [q-bio], Arms race, Biology, Evolutionary genetics, Mobile elements, Cellular life, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, Genetics, Viral evolution, Molecular Biology, Genetics (clinical), 030304 developmental biology, 0303 health sciences, Host defence, Biological Evolution, Interspersed Repetitive Sequences, DNA transposable elements, Evolutionary biology, Host-Pathogen Interactions, Molecular evolution, Mobile genetic elements, 030217 neurology & neurosurgery, Fitness cost
Abstract: All cellular life forms are afflicted by diverse genetic parasites, including viruses and other types of mobile genetic elements (MGEs), and have evolved multiple, diverse defence systems that protect them from MGE assault via different mechanisms. Here, we provide our perspectives on how recent evidence points to tight evolutionary connections between MGEs and defence systems that reach far beyond the proverbial arms race. Defence systems incur a fitness cost for the hosts; therefore, at least in prokaryotes, horizontal mobility of defence systems, mediated primarily by MGEs, is essential for their persistence. Moreover, defence systems themselves possess certain features of selfish elements. Common components of MGEs, such as site-specific nucleases, are ‘guns for hire’ that can also function as parts of defence mechanisms and are often shuttled between MGEs and defence systems. Thus, evolutionary and molecular factors converge to mould the multifaceted, inextricable connection between MGEs and anti-MGE defence systems. Incessant encounters of all cellular life forms with mobile genetic elements (MGEs) have driven the evolution of diverse defence mechanisms, including CRISPR–Cas and restriction–modification systems. In this Perspective, Koonin, Makarova, Wolf and Krupovic describe the surprisingly intricate interplay between MGEs and host defence systems. Not only do defence systems commonly show high horizontal mobility but many molecular components are ‘guns for hire’ that have been co-opted by defence systems from MGEs and vice versa.
Published: 2020

46. Improved reference genome of the arboviral vector Aedes albopictus

Author: J. Spencer Johnston, Pascal Miesen, Maria V. Sharakhova, Omar S. Akbari, D. A. Karagodin, Patrick Masterson, Jay Ghurye, Luciano V. Cosme, Umberto Palatini, Adam M. Phillippy, Anna-Bella Failloux, Ronald P. van Rij, James K. Biedler, Arang Rhie, Igor Antoshechkin, Mariangela Bonizzoni, Jacob E. Crawford, Sergey Koren, Jeremy Jenrette, Adalgisa Caccone, Reem A. Masri, Michele Marconcini, Zhijian Tu, Jeffrey R. Powell, Atashi Sharma, Rebecca Halbach, Stephanie Gamez, Elisa Pischedda, Flavia Krsticevic, Françoise Thibaud-Nissen, Philippos Aris Papathanos, Dipartimento di Biologia e Biotecnologie 'Lazzaro Spallanzani' = Department of Biology and Biotechnology [Univ di Pavia] (DBB UNIPV), Università degli Studi di Pavia = University of Pavia (UNIPV), Virginia Polytechnic Institute and State University [Blacksburg], Department of Ecology and Evolutionary Biology [New Haven], Yale University [New Haven], National Human Genome Research Institute (NHGRI), National Center for Biotechnology Information (NCBI), The Hebrew University of Jerusalem (HUJ), Texas A&M University [College Station], Radboud University Medical Center [Nijmegen], Verily Life Sciences Inc, California Institute of Technology (CALTECH), Arbovirus et Insectes Vecteurs - Arboviruses and Insect Vectors, Institut Pasteur [Paris] (IP), Siberian Branch of the Russian Academy of Sciences (SB RAS), University of California [San Diego] (UC San Diego), University of California (UC), Tomsk State University [Tomsk], National Biodefense Analysis and Countermeasures Center [Frederick], U.S. Social Security Administration, The authors would like to thank the following for their financial support of research: European Research Council (ERC-CoG 682394 to M. Bonizzoni, ERC-CoG 615680 to R.P. van Rij), Italian Ministry of Education, University and Research (FARE-MIUR project R1623HZAH5 to M. Bonizzoni and Dipartimenti Eccellenza Program 2018–2022 to Department of Biology and Biotechnology 'L. Spallanzani,' University of Pavia), Human Frontiers Science Foundation (Research Grant number RGP0007/2017) to M. Bonizzoni and R.P. van Rij, National Institutes of Health (R21AI135258 to M. Sharakova, 1R01AI151004-01 and 1DP2AI152071-01 to O.S. Akbari, R01AI32409 to A. Caccone), Defense Advanced Research Project Agency (DARPA) Safe Genes Program Grant (HR0011-17-2-0047) to O.S. Akbari, Netherlands Organization for Scientific Research (VICI grant number 016.VICI.170.090) to R.P. van Rij, Israeli Ministry of Science and Technology (3-16795 to P.A. Papathanos), Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health to J. Ghurye, A. Rhie, and A.M. Phillippy, Intramural Research Program of the National Library of Medicine, National Institutes of Health to F. Thibaud-Niessen, generous UCSD lab. startup funds to O.S. Akbari., We would like to thank Francesca Scolari and Patrizia Chiari for the mosquito maintenance., European Project: 682394,H2020,ERC-2015-CoG,NIRV_HOST_INT(2016), European Project: 615680,EC:FP7:ERC,ERC-2013-CoG,VIVARNASILENCING(2014), Dipartimento di Biologia e Biotecnologie ‘Lazzaro Spallanzani’, University of Pavia, University of Pavia, Institut Pasteur [Paris], and University of California
Subjects: lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], Sequence assembly, Viral integrations, Genome, 0302 clinical medicine, Genome Size, Aedes, Population differentiation, lcsh:QH301-705.5, 0303 health sciences, Chromosome Mapping, Biological Sciences, 3. Good health, Infectious Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, miRNAs, Infection, Sex locus, Biotechnology, Aedes albopictus, lcsh:QH426-470, albopictus, Bioinformatics, Developmental transcriptome, 1.1 Normal biological development and functioning, Ae, Locus (genetics), Mosquito Vectors, Computational biology, Biology, Small Interfering, Chromosomes, DNA sequencing, Vaccine Related, 03 medical and health sciences, Rare Diseases, All institutes and research themes of the Radboud University Medical Center, Underpinning research, Biodefense, Information and Computing Sciences, Genetics, Animals, Ae. albopictus, Gene, 030304 developmental biology, Prevention, Research, Human Genome, fungi, Immunity, biology.organism_classification, Human genetics, Insect Vectors, Vector-Borne Diseases, lcsh:Genetics, Emerging Infectious Diseases, Good Health and Well Being, lcsh:Biology (General), RNA, Generic health relevance, Transcriptome, Arboviruses, Environmental Sciences, piRNA clusters, 030217 neurology & neurosurgery, Reference genome
Abstract: Background The Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary approach to prevent mosquito-borne diseases. A reliable and accurate DNA sequence of the Ae. albopictus genome is essential to develop new approaches that involve genetic manipulation of mosquitoes. Results We use long-read sequencing methods and modern scaffolding techniques (PacBio, 10X, and Hi-C) to produce AalbF2, a dramatically improved assembly of the Ae. albopictus genome. AalbF2 reveals widespread viral insertions, novel microRNAs and piRNA clusters, the sex-determining locus, and new immunity genes, and enables genome-wide studies of geographically diverse Ae. albopictus populations and analyses of the developmental and stage-dependent network of expression data. Additionally, we build the first physical map for this species with 75% of the assembled genome anchored to the chromosomes. Conclusion The AalbF2 genome assembly represents the most up-to-date collective knowledge of the Ae. albopictus genome. These resources represent a foundation to improve understanding of the adaptation potential and the epidemiological relevance of this species and foster the development of innovative control measures.
Published: 2020

47. Phages build anti-defence barriers

Author: Mart Krupovic, Eugene V. Koonin, National Library of Medicine (NLM), National Institutes of Health [Bethesda] (NIH)-National Center for Biotechnology Information (NCBI), Virologie des archées - Archaeal Virology, Institut Pasteur [Paris], and Institut Pasteur [Paris] (IP)
Subjects: Microbiology (medical), MESH: Cell Nucleus, viruses, Immunology, Phage biology, Biology, Applied Microbiology and Biotechnology, Microbiology, Genome, Virus, 03 medical and health sciences, MESH: RNA, Genetics, CRISPR, Bacteriophages, 030304 developmental biology, 0303 health sciences, 030306 microbiology, Effector, MESH: DNA, Cell Biology, Restriction enzyme, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, MESH: Bacteriophages/genetics, MESH: Clustered Regularly Interspaced Short Palindromic Repeats
Abstract: Comment on : A jumbo phage that forms a nucleus-like structure evades CRISPR-Cas DNA targeting but is vulnerable to type III RNA-based immunity. [Nat Microbiol. 2020]; International audience; Two recent studies reveal a virus anti-defence strategy whereby large, ‘jumbo’ phages protect themselves from both restriction endonucleases and DNA-targeting CRISPR–Cas systems, but not from RNA-targeting ones, by encapsulating the phage genome inside the cell in a ‘nucleus’-like shell that is impenetrable for CRISPR effectors.
Published: 2020

48. Viral rhodopsins 1 are an unique family of light-gated cation channels

Author: R. Astashkin, G. A. Armeev, Natalia Yutin, Andreas Offenhäusser, Ekaterina Savelyeva, Kirill Kovalev, Igor Chizhov, Dmitrii Zabelskii, Francisco Rodriguez-Valera, Ernst Bamberg, Alexander Popov, Vladan Rankovic, Maksim Rulev, Dmitry Bratanov, Valentin Gordeliy, Alexey Alekseev, Michel Vivaudou, D V Soloviov, Riccardo Rosselli, Taras Balandin, Tatiana I. Rokitskaya, Eugene V. Koonin, Georg Büldt, Svetlana Vaganova, Ana-Sofia Eria-Oliveira, Yuri N. Antonenko, Tobias Moser, Mikhail P. Kirpichnikov, A. V. Rogachev, Thomas Mager, Dieter Willbold, Elizaveta Podolyak, Dmytro Volkov, Konstantin V. Shaitan, Institute of Biological Information Processing [Jülich] (IBI-7), Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Institute for Auditory Neuroscience and InnerEarLab, Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow, Hannover Medical School [Hannover] (MHH), National Center for Biotechnology Information (NCBI), European Synchrotron Radiation Facility (ESRF), Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University (MSU), Max-Planck-Institut für Biophysik - Max Planck Institute of Biophysics (MPIBP), Max-Planck-Gesellschaft, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández [Elche] (UMH), Lomonosov Moscow State University, Biological Faculty, N. N. Semenov Institute of Chemical Physics, Russian Academy of Sciences [Moscow] (RAS), InnerEarLab, Department of Otolaryngology and Center for Molecular Physiology of the Brain-Georg-August-University = Georg-August-Universität Göttingen, National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Bethesda, Md, National Institutes of Health [Bethesda] (NIH), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), ANR-19-CE11-0026,Viral_Rhodopsins,Rhodopsines virales: Structure, Fonction, et Nouveaux Outils pour l'Optogénétique(2019), and Department of Otolaryngology and Center for Molecular Physiology of the Brain-University of Göttingen - Georg-August-Universität Göttingen
Subjects: 0301 basic medicine, genetic structures, Light, Protein Conformation, General Physics and Astronomy, Channelrhodopsin, 0302 clinical medicine, Protein structure, X-Ray Diffraction, Phototaxis, lcsh:Science, Cells, Cultured, Phylogeny, Neurons, Multidisciplinary, biology, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Chemistry, Cell biology, Rhodopsin, ddc:500, Ion Channel Gating, Science, Optogenetics, Nucleocytoplasmic large DNA viruses, Virus-host interactions, Article, General Biochemistry, Genetics and Molecular Biology, Structure-Activity Relationship, Viral Proteins, 03 medical and health sciences, Channelrhodopsins, Phylogenetics, Cations, Animals, Humans, 14. Life underwater, Rats, Wistar, Ion transport, HEK 293 cells, fungi, General Chemistry, biology.organism_classification, HEK293 Cells, 030104 developmental biology, Phytoplankton, biology.protein, lcsh:Q, Calcium, sense organs, 030217 neurology & neurosurgery
Abstract: Phytoplankton is the base of the marine food chain as well as oxygen and carbon cycles and thus plays a global role in climate and ecology. Nucleocytoplasmic Large DNA Viruses that infect phytoplankton organisms and regulate the phytoplankton dynamics encompass genes of rhodopsins of two distinct families. Here, we present a functional and structural characterization of two proteins of viral rhodopsin group 1, OLPVR1 and VirChR1. Functional analysis of VirChR1 shows that it is a highly selective, Na+/K+-conducting channel and, in contrast to known cation channelrhodopsins, it is impermeable to Ca2+ ions. We show that, upon illumination, VirChR1 is able to drive neural firing. The 1.4 Å resolution structure of OLPVR1 reveals remarkable differences from the known channelrhodopsins and a unique ion-conducting pathway. Thus, viral rhodopsins 1 represent a unique, large group of light-gated channels (viral channelrhodopsins, VirChR1s). In nature, VirChR1s likely mediate phototaxis of algae enhancing the host anabolic processes to support virus reproduction, and therefore, might play a major role in global phytoplankton dynamics. Moreover, VirChR1s have unique potential for optogenetics as they lack possibly noxious Ca2+ permeability., Nucleocytoplasmic Large DNA Viruses (NCLDV) that infect algae encode two distinct families of microbial rhodopsins. Here, the authors characterise two proteins form the viral rhodopsin group 1 OLPVR1 and VirChR1, present the 1.4 Å crystal structure of OLPVR1 and show that viral rhodopsins 1 are light-gated cation channels.
Published: 2020
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49. Multiple origins of prokaryotic and eukaryotic single-stranded DNA viruses from bacterial and archaeal plasmids

Author: Darius Kazlauskas, Arvind Varsani, Eugene V. Koonin, Mart Krupovic, Vilnius University [Vilnius], The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life sciences, Arizona State University [Tempe] (ASU), Structural Biology Research Unit [Cape Town], Department of Integrative Biomedical Sciences [Cape Town], University of Cape Town-University of Cape Town, National Center for Biotechnology Information (NCBI), Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), and Institut Pasteur [Paris] (IP)
Subjects: 0301 basic medicine, Molecular biology, Science, viruses, [SDV]Life Sciences [q-bio], Single-stranded (ss) DNA viruses, HUH endonuclease superfamily, prokaryotic DNA viruses, DNA, Single-Stranded, General Physics and Astronomy, Genome, Viral, 02 engineering and technology, Biology, Genome, Article, General Biochemistry, Genetics and Molecular Biology, Evolution, Molecular, Parvovirus, 03 medical and health sciences, chemistry.chemical_compound, Plasmid, Virology, Complementary DNA, Human virome, lcsh:Science, Papillomaviridae, Gene, Genetics, Multidisciplinary, Bacteria, Base Sequence, DNA Helicases, RNA, General Chemistry, biochemical phenomena, metabolism, and nutrition, 021001 nanoscience & nanotechnology, Archaea, 030104 developmental biology, chemistry, Prokaryotic DNA replication, DNA, Viral, bacteria, Molecular evolution, lcsh:Q, Polyomavirus, 0210 nano-technology, Sequence Alignment, DNA, Plasmids
Abstract: Single-stranded (ss) DNA viruses are a major component of the earth virome. In particular, the circular, Rep-encoding ssDNA (CRESS-DNA) viruses show high diversity and abundance in various habitats. By combining sequence similarity network and phylogenetic analyses of the replication proteins (Rep) belonging to the HUH endonuclease superfamily, we show that the replication machinery of the CRESS-DNA viruses evolved, on three independent occasions, from the Reps of bacterial rolling circle-replicating plasmids. The CRESS-DNA viruses emerged via recombination between such plasmids and cDNA copies of capsid genes of eukaryotic positive-sense RNA viruses. Similarly, the rep genes of prokaryotic DNA viruses appear to have evolved from HUH endonuclease genes of various bacterial and archaeal plasmids. Our findings also suggest that eukaryotic polyomaviruses and papillomaviruses with dsDNA genomes have evolved via parvoviruses from CRESS-DNA viruses. Collectively, our results shed light on the complex evolutionary history of a major class of viruses revealing its polyphyletic origins., Most single-stranded DNA viruses have small genomes replicated by rolling circle mechanism which is initiated by the Rep protein. Here, using sequence similarity network and phylogenetic analyses, Kazlauskas et al. show that viral Reps evolved from Reps of bacterial and archaeal plasmids on multiple independent occasions.
Published: 2019

50. Identification of the m6Am Methyltransferase PCIF1 Reveals the Location and Functions of m6Am in the Transcriptome

Author: Françoise Debart, Diana Toczydlowska-Socha, Théo Guez, Samie R. Jaffrey, Jean-Jacques Vasseur, Noa Liberman, Ken Takashima, Konstantinos Boulias, Eric L. Greer, Ben R Hawley, L. Aravind, Sara Zaccara, Institut des Biomolécules Max Mousseron [Pôle Chimie Balard] (IBMM), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), and National Center for Biotechnology Information (NCBI)
Subjects: Gene isoform, Adenosine, Methyltransferase, Future studies, mRNA translation, m 6 A, m(6)Am, Computational biology, Biology, m(6)A, Methylation, PCIF1, Article, Transcriptome, mRNA methylation, 03 medical and health sciences, 0302 clinical medicine, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Humans, Nucleotide, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, RNA, Messenger, mRNA stability, RNA Processing, Post-Transcriptional, Molecular Biology, Adaptor Proteins, Signal Transducing, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, m 6 Am, 030302 biochemistry & molecular biology, Nuclear Proteins, Cell Biology, Methyltransferases, chemistry, Protein Biosynthesis, MRNA Isoforms, Identification (biology), MRNA methylation, Transcription Initiation Site, 030217 neurology & neurosurgery, Function (biology)
Abstract: mRNAs are regulated by nucleotide modifications that influence their cellular fate. Two of the most abundant modified nucleotides are N6-methyladenosine (m6A), found within mRNAs, and N6,2-O-dimethyladenosine (m6Am), which is found at the first-transcribed nucleotide. A long-standing challenge has been distinguishing these similar modifications in transcriptome-wide mapping studies. Here we identify and biochemically characterize, PCIF1, the methyltransferase that generates m6Am. We find that PCIF1 binds and is dependent on the m7G cap. By depleting PCIF1, we definitively identified m6Am sites and generated transcriptome-wide maps that are selective for m6Am and m6A. We find that m6A and m6Am misannotations largely arise from mRNA isoforms with alternate transcription-start sites. These isoforms contain m6Am that appear to map to internal sites, increasing the likelihood of misannotation. Using the new m6Am annotations, we find that depleting m6Am does not affect mRNA translation but reduces the stability of a subset of m6Am-annotated mRNAs. The discovery of PCIF1 and our accurate mapping technique will facilitate future studies to characterize m6Ams function.
Published: 2019

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